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 84 with the SMILES code CC1=CC=C(\C=C\C(O)=O)C=C1

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 45.37 α = 90
b = 73.14 β = 109.72
c = 52.8 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 -- 2012-11-16
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
1.38 42.71 99.0 0.085 -- -- 4.224 -- 66098 -- -3.0 8.93
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)
1.38 1.46 97.8 0.69 -- 2.11 -- --

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 1.38 36.883 -- 1.99 -- 66096 3305 99.1 -- 0.1365 0.135 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 1.3796 1.3993 -- 131 2496 0.2 0.2725 -- 97.0
X Ray Diffraction 1.3993 1.4202 -- 139 2632 0.1888 0.2458 -- 98.0
X Ray Diffraction 1.4202 1.4424 -- 134 2555 0.1732 0.2097 -- 98.0
X Ray Diffraction 1.4424 1.466 -- 137 2606 0.1586 0.2072 -- 98.0
X Ray Diffraction 1.466 1.4913 -- 136 2578 0.154 0.1904 -- 98.0
X Ray Diffraction 1.4913 1.5184 -- 136 2578 0.1455 0.2413 -- 99.0
X Ray Diffraction 1.5184 1.5476 -- 137 2620 0.1386 0.1911 -- 99.0
X Ray Diffraction 1.5476 1.5792 -- 136 2573 0.1287 0.1736 -- 99.0
X Ray Diffraction 1.5792 1.6136 -- 138 2619 0.1177 0.1651 -- 99.0
X Ray Diffraction 1.6136 1.6511 -- 137 2599 0.115 0.1629 -- 99.0
X Ray Diffraction 1.6511 1.6924 -- 138 2629 0.1134 0.1352 -- 99.0
X Ray Diffraction 1.6924 1.7381 -- 137 2603 0.1113 0.1589 -- 99.0
X Ray Diffraction 1.7381 1.7893 -- 137 2613 0.1119 0.1481 -- 99.0
X Ray Diffraction 1.7893 1.847 -- 138 2623 0.1119 0.1599 -- 100.0
X Ray Diffraction 1.847 1.913 -- 139 2633 0.1125 0.1642 -- 99.0
X Ray Diffraction 1.913 1.9896 -- 137 2601 0.1065 0.1412 -- 99.0
X Ray Diffraction 1.9896 2.0802 -- 139 2644 0.1115 0.1311 -- 100.0
X Ray Diffraction 2.0802 2.1898 -- 139 2637 0.1117 0.133 -- 100.0
X Ray Diffraction 2.1898 2.327 -- 139 2634 0.1208 0.1736 -- 100.0
X Ray Diffraction 2.327 2.5066 -- 139 2655 0.1296 0.1373 -- 100.0
X Ray Diffraction 2.5066 2.7588 -- 139 2636 0.1361 0.1528 -- 100.0
X Ray Diffraction 2.7588 3.1578 -- 140 2657 0.1462 0.1601 -- 100.0
X Ray Diffraction 3.1578 3.9778 -- 140 2659 0.1557 0.1782 -- 100.0
X Ray Diffraction 3.9778 36.8961 -- 143 2711 0.1559 0.1607 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 11.5206
RMS Deviations
Key Refinement Restraint Deviation
f_bond_d 0.007
f_plane_restr 0.006
f_dihedral_angle_d 10.771
f_angle_d 1.161
f_chiral_restr 0.068
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2369
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 249

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