X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 4.6
Temperature 290.0
Details 0.1 M ammonium acetate, 0.1 M sodium acetate, 24-30% PEG 4000; crystal obtained by streak-seeding and soaked with 90 mM of fragment 263 with the SMILES code CC1(C)CC(CC(C)(C)N1)NC(=O)[C@@H]1CCC=CC1

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 45.19 α = 90
b = 72.73 β = 90
c = 104.4 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS 6M -- 2013-07-18
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON BESSY BEAMLINE 14.1 0.918409 BESSY 14.1

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot
1.28 45.19 98.3 0.061 -- -- 7.184 -- 88277 -- -3.0 10.96
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
1.28 1.36 95.5 0.49 -- 3.52 -- --

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
MOLECULAR REPLACEMENT 1.278 34.339 -- 1.37 -- 88273 4413 98.32 -- 0.1366 0.1358 0.1515 RANDOM
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 1.2778 1.2923 -- 130 2469 0.1781 0.1963 -- 88.0
X Ray Diffraction 1.2923 1.3075 -- 142 2708 0.1625 0.1876 -- 97.0
X Ray Diffraction 1.3075 1.3235 -- 145 2753 0.1589 0.1927 -- 97.0
X Ray Diffraction 1.3235 1.3402 -- 144 2736 0.1515 0.163 -- 98.0
X Ray Diffraction 1.3402 1.3579 -- 145 2753 0.1438 0.1921 -- 98.0
X Ray Diffraction 1.3579 1.3765 -- 144 2733 0.1358 0.1956 -- 98.0
X Ray Diffraction 1.3765 1.3961 -- 144 2734 0.1253 0.1583 -- 98.0
X Ray Diffraction 1.3961 1.417 -- 146 2775 0.1204 0.1392 -- 98.0
X Ray Diffraction 1.417 1.4391 -- 145 2760 0.1167 0.1449 -- 98.0
X Ray Diffraction 1.4391 1.4627 -- 146 2769 0.1134 0.1543 -- 98.0
X Ray Diffraction 1.4627 1.4879 -- 144 2744 0.1062 0.1467 -- 98.0
X Ray Diffraction 1.4879 1.515 -- 147 2796 0.11 0.134 -- 98.0
X Ray Diffraction 1.515 1.5441 -- 145 2742 0.1071 0.1282 -- 98.0
X Ray Diffraction 1.5441 1.5756 -- 147 2790 0.1096 0.1291 -- 99.0
X Ray Diffraction 1.5756 1.6099 -- 147 2798 0.1069 0.1421 -- 99.0
X Ray Diffraction 1.6099 1.6473 -- 147 2792 0.1078 0.1398 -- 99.0
X Ray Diffraction 1.6473 1.6885 -- 147 2804 0.1089 0.1488 -- 99.0
X Ray Diffraction 1.6885 1.7342 -- 147 2787 0.1108 0.1342 -- 99.0
X Ray Diffraction 1.7342 1.7852 -- 147 2801 0.1136 0.135 -- 99.0
X Ray Diffraction 1.7852 1.8428 -- 149 2823 0.1118 0.1312 -- 99.0
X Ray Diffraction 1.8428 1.9087 -- 148 2815 0.1173 0.1357 -- 99.0
X Ray Diffraction 1.9087 1.9851 -- 149 2823 0.1218 0.1533 -- 99.0
X Ray Diffraction 1.9851 2.0754 -- 149 2843 0.124 0.1542 -- 99.0
X Ray Diffraction 2.0754 2.1848 -- 149 2830 0.1249 0.1297 -- 100.0
X Ray Diffraction 2.1848 2.3217 -- 151 2856 0.128 0.1341 -- 99.0
X Ray Diffraction 2.3217 2.5009 -- 150 2856 0.1393 0.14 -- 100.0
X Ray Diffraction 2.5009 2.7525 -- 152 2884 0.1441 0.1513 -- 100.0
X Ray Diffraction 2.7525 3.1506 -- 153 2902 0.1492 0.1518 -- 100.0
X Ray Diffraction 3.1506 3.9684 -- 154 2928 0.1543 0.1715 -- 100.0
X Ray Diffraction 3.9684 34.3519 -- 160 3056 0.1748 0.1696 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 13.8128
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.006
f_bond_d 0.007
f_chiral_restr 0.073
f_angle_d 1.178
f_dihedral_angle_d 10.961
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2369
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 239

Software

Software
Software Name Purpose
XDS data scaling
PHENIX refinement
PHASER phasing version: 2.5.7
PDB_EXTRACT data extraction version: 3.20
XDS data reduction