PAIREF - results 1H87

Input parameters

Project:

1H87_dui

High resolution diffraction limits:

1.72 Å, 1.60 Å, 1.50 Å, 1.40 Å, 1.30 Å, 1.20 Å

Initial structure model:

1H87_single_shaken.pdb

Merged diffraction data:

1H87_dui_R.mtz

Unmerged diffraction data:

1H87_dui_unmerged.mtz

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.

Run details and program versions

Working directory:

/public/pairef_datasets/publication_examples/3-1_SIM/pairef_1H87_dui

Run date and time:

2020-05-28 09:55:17

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: 1H87_dui_R-values.csv

# Shell      Rwork(init) Rwork(fin) Rwork(diff)   Rfree(init) Rfree(fin) Rfree(diff)
1.72A->1.60A      0.0606     0.0592     -0.0014        0.0711     0.0679     -0.0032
1.60A->1.50A      0.0654     0.0653     -0.0001        0.0745     0.0734     -0.0011
1.50A->1.40A      0.0733     0.0733      0.0000        0.0811     0.0805     -0.0006
1.40A->1.30A      0.0848     0.0847     -0.0001        0.0938     0.0934     -0.0004
1.30A->1.20A      0.1047     0.1049      0.0002        0.1112     0.1113      0.0001

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

Raw data: 1H87_dui_Rgap.csv

Note: The R-values were calculated at 1.72 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 34.57 3.43 11223 1755 6.39 99.83 726.0 27.2 0.060 0.066 0.027 0.985 0.207 0.9962 02 3.43 2.43 20639 2965 6.96 99.83 264.6 18.8 0.059 0.064 0.024 0.997 0.618 0.9992 03 2.43 1.98 25070 3846 6.52 100.00 108.4 9.5 0.105 0.114 0.043 0.988 0.404 0.9970 04 1.98 1.72 30516 4336 7.04 99.93 40.8 4.0 0.235 0.254 0.094 0.971 0.156 0.9926 05 1.72 1.60 19736 3054 6.46 100.00 20.7 2.0 0.431 0.468 0.180 0.901 0.080 0.9736 06 1.60 1.50 19671 3305 5.95 99.70 13.1 1.1 0.731 0.800 0.317 0.752 0.008 0.9265 07 1.50 1.40 23094 4325 5.34 99.61 8.9 0.6 1.110 1.230 0.515 0.513 0.024 0.8235 08 1.40 1.30 16791 5345 3.14 93.44 5.3 0.3 1.890 2.233 1.153 0.179 0.021 0.5510 09 1.30 1.20 3690 2566 1.44 33.03 2.7 0.1 3.379 4.476 2.900 0.034 -0.384 0.2564

Statistics vs. cycle

Log file from refinement at 1.72 Å
Structure model refined at 1.72 Å PDB mmCIF

Log file from refinement at 1.60 Å
Structure model refined at 1.60 Å PDB mmCIF

Log file from refinement at 1.50 Å
Structure model refined at 1.50 Å PDB mmCIF

Log file from refinement at 1.40 Å
Structure model refined at 1.40 Å PDB mmCIF

Log file from refinement at 1.30 Å
Structure model refined at 1.30 Å PDB mmCIF

Log file from refinement at 1.20 Å
Structure model refined at 1.20 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 - 1H87_dui