PAIREF - results BO

Input parameters

Project:

BO_from2-80A

High resolution diffraction limits:

2.80 Å, 2.70 Å, 2.59 Å, 2.50 Å, 2.40 Å, 2.30 Å

Initial structure model:

BO_edit94_refmac1.pdb

Merged diffraction data:

BO_R.mtz

Unmerged diffraction data:

XDS_ASCII.HKL

Crystallographic restraints:

merge_TRP-HIS_FC6.cif

Keywords for REFMAC5:

setting.com

Weight matrix for REFMAC5:

0.0480

Number of refinement cycles that will be performed in every resolution step:

Number of pre-refinement cycles that will be performed before the paired refinement protocol:

Data with FreeRflag set 0 will be excluded during refinement.

Modification of the input structure model:

Reset B-factors to the mean value
Randomize coordinates with the given mean error value: 0.02

Run details and program versions

Working directory:

/public/pairef_datasets/publication_examples/3-6_BO/pairef_BO_from2-80A

Run date and time:

2020-05-28 11:42:35

user@host:

maly@localhost

PAIREF version:

1.1.0

REFMAC5 version:

5.8.0258

Python version and executable:

2.7.15 /protein2/phenix/phenix-1.16-3546/build/../conda_base/bin/python2.7

matplotlib version:

2.2.3

Overall values

Raw data: BO_from2-80A_R-values.csv

# Shell      Rwork(init) Rwork(fin) Rwork(diff)   Rfree(init) Rfree(fin) Rfree(diff)
2.80A->2.70A      0.1533     0.1552      0.0019        0.2282     0.2274     -0.0008
2.70A->2.59A      0.1625     0.1631      0.0006        0.2350     0.2323     -0.0027
2.59A->2.50A      0.1765     0.1757     -0.0008        0.2426     0.2428      0.0002
2.50A->2.40A      0.1882     0.1873     -0.0009        0.2514     0.2525      0.0011
2.40A->2.30A      0.2001     0.2000     -0.0001        0.2625     0.2641      0.0016

Note: For each incremental step of resolution from X->Y, the R-values were calculated at resolution X.

Raw data: BO_from2-80A_Rgap.csv

Note: The R-values were calculated at 2.80 Å resolution.

Merging statistics

#shell d_max d_min #obs #uniq mult. %comp <I> <I/sI> r_mrg r_meas r_pim cc1/2 cc_ano cc* 01 47.35 8.16 12463 1641 7.59 99.58 390.7 41.2 0.037 0.040 0.014 0.999 0.280 0.9997 02 8.16 5.87 21992 2683 8.20 100.00 196.2 29.0 0.062 0.066 0.023 0.998 0.122 0.9995 03 5.87 4.82 28271 3388 8.34 100.00 233.3 28.7 0.062 0.066 0.023 0.998 0.038 0.9995 04 4.82 4.19 33174 3950 8.40 100.00 263.0 28.1 0.063 0.068 0.023 0.998 0.027 0.9995 05 4.19 3.75 38299 4533 8.45 100.00 213.7 22.9 0.082 0.087 0.030 0.998 -0.003 0.9995 06 3.75 3.43 41442 4886 8.48 99.98 134.7 15.4 0.129 0.138 0.047 0.995 -0.000 0.9987 07 3.43 3.18 44981 5292 8.50 100.00 88.2 10.2 0.206 0.219 0.074 0.988 0.003 0.9970 08 3.18 2.97 50512 5936 8.51 100.00 54.5 6.6 0.324 0.345 0.117 0.971 0.004 0.9926 09 2.97 2.80 52338 6147 8.51 100.00 33.6 4.2 0.530 0.564 0.192 0.927 0.019 0.9809 10 2.80 2.70 37116 4393 8.45 100.00 24.0 3.0 0.745 0.793 0.271 0.852 0.017 0.9592 11 2.70 2.59 38450 5619 6.84 100.00 17.0 1.9 1.002 1.085 0.411 0.694 0.012 0.9052 12 2.59 2.50 27420 5353 5.12 99.79 13.5 1.2 1.198 1.338 0.584 0.524 0.025 0.8293 13 2.50 2.40 27592 6777 4.07 97.54 11.2 0.9 1.396 1.613 0.785 0.283 0.008 0.6642 14 2.40 2.30 24246 7300 3.32 89.13 8.7 0.6 1.795 2.145 1.140 0.176 0.007 0.5471

Statistics vs. cycle

Log file from refinement at 2.80 Å
Structure model refined at 2.80 Å PDB mmCIF

Log file from refinement at 2.70 Å
Structure model refined at 2.70 Å PDB mmCIF

Log file from refinement at 2.59 Å
Structure model refined at 2.59 Å PDB mmCIF

Log file from refinement at 2.50 Å
Structure model refined at 2.50 Å PDB mmCIF

Log file from refinement at 2.40 Å
Structure model refined at 2.40 Å PDB mmCIF

Log file from refinement at 2.30 Å
Structure model refined at 2.30 Å PDB mmCIF

References

Paired refinement under control of PAIREF. M. Maly, K. Diederichs, J. Dohnalek, P. Kolenko (2020) IUCrJ (to be published)

Overview of the CCP4 suite and current developments. Collaborative Computational Project, Number 4 (2011) Acta Cryst. D67:235–242

REFMAC5 for the refinement of macromolecular crystal structures. G.N. Murshudov, P. Skubak, A.A. Lebedev, N.S. Pannu, R.A. Steiner, R.A. Nicholls, M.D. Winn, F. Long, A.A. Vagin (2011) Acta Cryst. D67:355–367

SFCHECK: a unified set of procedures for evaluating the quality of macromolecular structure-factor data and their agreement with the atomic model. A.A. Vaguine, J. Richelle, S.J. Wodak (1999) Acta Cryst. D55:191–205

The Computational Crystallography Toolbox: crystallographic algorithms in a reusable software framework. R.W. Grosse-Kunstleve, N.K. Sauter, N.W. Moriarty, P.D. Adams (2002) J. Appl. Crystallogr. 35:126–136

Linking crystallographic model and data quality. P.A. Karplus & K. Diederichs (2012) Science 336:1030–3

Assessing and maximizing data quality in macromolecular crystallography. P.A. Karplus & K. Diederichs (2015) Cur. Op. in Str. Biology 34:60–68

Better models by discarding data? P.A. Karplus & K. Diederichs (2013) Acta Cryst. D59:1215–1222

Results - BO_from2-80A