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 232 with the SMILES code CC(C)(C)N1CN=C2S[C@](C)(CO)C(=O)N2C1

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 45.26 α = 90
b = 72.87 β = 109.39
c = 52.68 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MAR CCD 165 mm -- 2014-02-15
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON BESSY BEAMLINE 14.3 0.8944 BESSY 14.3

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
1.42 42.7 99.1 0.06 -- -- 4.203 -- 60646 -- -3.0 10.02
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)
1.42 1.5 96.9 0.472 -- 3.5 -- --

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 1.418 39.513 -- 1.37 -- 60631 3032 99.23 -- 0.1301 0.1289 0.1533 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 1.4179 1.44 -- 126 2395 0.1569 0.2009 -- 91.0
X Ray Diffraction 1.44 1.4636 -- 138 2619 0.1472 0.2028 -- 99.0
X Ray Diffraction 1.4636 1.4889 -- 136 2589 0.1433 0.191 -- 99.0
X Ray Diffraction 1.4889 1.516 -- 137 2604 0.1345 0.2136 -- 99.0
X Ray Diffraction 1.516 1.5451 -- 139 2625 0.1258 0.1646 -- 99.0
X Ray Diffraction 1.5451 1.5767 -- 137 2600 0.1179 0.1705 -- 100.0
X Ray Diffraction 1.5767 1.6109 -- 137 2616 0.1133 0.1624 -- 99.0
X Ray Diffraction 1.6109 1.6484 -- 137 2605 0.1115 0.1605 -- 99.0
X Ray Diffraction 1.6484 1.6896 -- 139 2641 0.1045 0.1445 -- 100.0
X Ray Diffraction 1.6896 1.7353 -- 139 2635 0.1026 0.1563 -- 100.0
X Ray Diffraction 1.7353 1.7864 -- 137 2603 0.1039 0.1398 -- 100.0
X Ray Diffraction 1.7864 1.844 -- 138 2624 0.102 0.1361 -- 100.0
X Ray Diffraction 1.844 1.9099 -- 140 2649 0.1014 0.1543 -- 100.0
X Ray Diffraction 1.9099 1.9864 -- 136 2599 0.1022 0.1141 -- 100.0
X Ray Diffraction 1.9864 2.0768 -- 140 2646 0.1043 0.1286 -- 100.0
X Ray Diffraction 2.0768 2.1863 -- 139 2646 0.1051 0.1287 -- 100.0
X Ray Diffraction 2.1863 2.3233 -- 138 2623 0.116 0.1279 -- 100.0
X Ray Diffraction 2.3233 2.5026 -- 140 2667 0.1288 0.1343 -- 100.0
X Ray Diffraction 2.5026 2.7544 -- 138 2619 0.135 0.1815 -- 100.0
X Ray Diffraction 2.7544 3.1528 -- 140 2650 0.1492 0.1664 -- 100.0
X Ray Diffraction 3.1528 3.9717 -- 139 2655 0.1524 0.1641 -- 100.0
X Ray Diffraction 3.9717 39.528 -- 142 2689 0.1572 0.1497 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 13.406
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.006
f_dihedral_angle_d 10.874
f_bond_d 0.007
f_angle_d 1.179
f_chiral_restr 0.069
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2369
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 204

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