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 251 with the SMILES code C[C@H]1C[C@H]1C(=O)NCC1=CC=C(C=C1)N1CCCC1=O

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 45.34 α = 90
b = 73.23 β = 109.31
c = 52.77 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
PIXEL DECTRIS PILATUS 6M -- 2013-04-04
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON BESSY BEAMLINE 14.1 0.91841 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 42.79 99.3 0.05 0.05 7.75 3.4 82272 82272 -- -- 10.32
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 1.35 99.1 0.225 0.225 3.2 3.5 11970

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 1.284 41.181 -- 1.36 -- 82244 4110 99.25 -- 0.1219 0.121 0.1403 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 1.284 1.2991 -- 126 2676 0.1282 0.1505 -- 99.0
X Ray Diffraction 1.2991 1.3149 -- 166 2633 0.1211 0.1329 -- 99.0
X Ray Diffraction 1.3149 1.3316 -- 139 2739 0.113 0.1597 -- 99.0
X Ray Diffraction 1.3316 1.3491 -- 141 2640 0.1123 0.144 -- 99.0
X Ray Diffraction 1.3491 1.3676 -- 124 2747 0.1092 0.1586 -- 99.0
X Ray Diffraction 1.3676 1.3871 -- 151 2653 0.1056 0.1287 -- 99.0
X Ray Diffraction 1.3871 1.4078 -- 137 2657 0.1055 0.1227 -- 99.0
X Ray Diffraction 1.4078 1.4298 -- 137 2706 0.0991 0.1334 -- 99.0
X Ray Diffraction 1.4298 1.4533 -- 147 2661 0.0987 0.1279 -- 99.0
X Ray Diffraction 1.4533 1.4783 -- 131 2669 0.0954 0.1317 -- 100.0
X Ray Diffraction 1.4783 1.5052 -- 163 2693 0.0969 0.1274 -- 100.0
X Ray Diffraction 1.5052 1.5342 -- 141 2689 0.0895 0.1257 -- 100.0
X Ray Diffraction 1.5342 1.5655 -- 133 2715 0.093 0.1225 -- 99.0
X Ray Diffraction 1.5655 1.5995 -- 131 2699 0.09 0.1162 -- 99.0
X Ray Diffraction 1.5995 1.6367 -- 133 2675 0.0907 0.1148 -- 99.0
X Ray Diffraction 1.6367 1.6777 -- 106 2720 0.0954 0.1207 -- 99.0
X Ray Diffraction 1.6777 1.723 -- 145 2658 0.0957 0.1237 -- 99.0
X Ray Diffraction 1.723 1.7737 -- 133 2715 0.0977 0.1366 -- 100.0
X Ray Diffraction 1.7737 1.831 -- 166 2694 0.0976 0.1104 -- 100.0
X Ray Diffraction 1.831 1.8964 -- 159 2654 0.0995 0.1043 -- 99.0
X Ray Diffraction 1.8964 1.9724 -- 152 2726 0.0993 0.1113 -- 100.0
X Ray Diffraction 1.9724 2.0621 -- 142 2680 0.1013 0.1127 -- 99.0
X Ray Diffraction 2.0621 2.1708 -- 160 2668 0.0999 0.1238 -- 99.0
X Ray Diffraction 2.1708 2.3068 -- 141 2701 0.1109 0.1233 -- 100.0
X Ray Diffraction 2.3068 2.4849 -- 139 2724 0.1168 0.1261 -- 100.0
X Ray Diffraction 2.4849 2.735 -- 151 2711 0.129 0.1456 -- 99.0
X Ray Diffraction 2.735 3.1306 -- 126 2707 0.136 0.1377 -- 99.0
X Ray Diffraction 3.1306 3.9437 -- 141 2729 0.1512 0.1633 -- 100.0
X Ray Diffraction 3.9437 41.2019 -- 149 2795 0.1813 0.2141 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 13.0221
RMS Deviations
Key Refinement Restraint Deviation
f_bond_d 0.006
f_dihedral_angle_d 10.749
f_plane_restr 0.006
f_chiral_restr 0.071
f_angle_d 1.2
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2369
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 225

Software

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