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 220 with the SMILES code CC1=CC(Br)=CC=C1NC(=O)C(F)(F)F

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 45.4 α = 90
b = 73.02 β = 109.38
c = 52.83 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 MARMOSAIC 225 mm CCD -- 2013-04-18
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON BESSY BEAMLINE 14.2 0.91841 BESSY 14.2

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
1.33 42.83 99.6 0.068 -- -- 3.728 -- 74444 -- -3.0 9.36
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)
1.33 1.41 99.0 0.684 -- 2.08 -- --

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 1.329 29.453 -- 2.0 -- 74443 3723 99.73 -- 0.1393 0.138 0.1648 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 1.3294 1.3462 -- 132 2509 0.2318 0.2688 -- 97.0
X Ray Diffraction 1.3462 1.3639 -- 139 2639 0.2099 0.2729 -- 100.0
X Ray Diffraction 1.3639 1.3826 -- 137 2605 0.2042 0.2238 -- 100.0
X Ray Diffraction 1.3826 1.4024 -- 137 2591 0.1936 0.217 -- 100.0
X Ray Diffraction 1.4024 1.4233 -- 139 2637 0.1828 0.2318 -- 100.0
X Ray Diffraction 1.4233 1.4455 -- 135 2568 0.1688 0.242 -- 100.0
X Ray Diffraction 1.4455 1.4692 -- 139 2642 0.1543 0.2026 -- 100.0
X Ray Diffraction 1.4692 1.4946 -- 138 2619 0.1449 0.1607 -- 100.0
X Ray Diffraction 1.4946 1.5217 -- 137 2602 0.1336 0.1881 -- 100.0
X Ray Diffraction 1.5217 1.551 -- 138 2632 0.1312 0.1722 -- 100.0
X Ray Diffraction 1.551 1.5827 -- 137 2598 0.1293 0.1752 -- 100.0
X Ray Diffraction 1.5827 1.6171 -- 138 2632 0.1239 0.1793 -- 100.0
X Ray Diffraction 1.6171 1.6547 -- 137 2605 0.1177 0.1616 -- 100.0
X Ray Diffraction 1.6547 1.6961 -- 139 2631 0.1089 0.148 -- 100.0
X Ray Diffraction 1.6961 1.7419 -- 138 2624 0.107 0.1518 -- 100.0
X Ray Diffraction 1.7419 1.7932 -- 137 2609 0.1055 0.1463 -- 100.0
X Ray Diffraction 1.7932 1.851 -- 138 2615 0.1058 0.1271 -- 100.0
X Ray Diffraction 1.851 1.9172 -- 139 2634 0.1077 0.1411 -- 100.0
X Ray Diffraction 1.9172 1.9939 -- 137 2612 0.1067 0.132 -- 100.0
X Ray Diffraction 1.9939 2.0847 -- 138 2629 0.1086 0.1326 -- 100.0
X Ray Diffraction 2.0847 2.1945 -- 139 2627 0.1101 0.1473 -- 100.0
X Ray Diffraction 2.1945 2.332 -- 138 2626 0.1211 0.1512 -- 100.0
X Ray Diffraction 2.332 2.5119 -- 139 2651 0.1325 0.1443 -- 100.0
X Ray Diffraction 2.5119 2.7646 -- 138 2608 0.1366 0.1567 -- 100.0
X Ray Diffraction 2.7646 3.1642 -- 139 2639 0.1443 0.1287 -- 100.0
X Ray Diffraction 3.1642 3.985 -- 139 2647 0.1542 0.1652 -- 100.0
X Ray Diffraction 3.985 29.4605 -- 142 2689 0.1663 0.1981 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 12.054
RMS Deviations
Key Refinement Restraint Deviation
f_bond_d 0.007
f_angle_d 1.156
f_chiral_restr 0.071
f_dihedral_angle_d 10.89
f_plane_restr 0.005
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2369
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 209

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