X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.3
Temperature 294.0
Details 0.1 M TRIS-HCL, 0.2 M NaCl, 0.9 M K/Na Tartrate, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 294K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 104.06 α = 90
b = 97.13 β = 117.38
c = 108.15 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
AREA DETECTOR PSI PILATUS 6M -- 2012-04-04
Diffraction Radiation
Monochromator Protocol
Liquid nitrogen-cooled double Si(111) crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL12-2 0.9795 SSRL BL12-2

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
1.75 50 97.7 -- -- -- -- -- 188791 0.0 0.0 20.34

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 1.75 48.566 -- 1.35 -- 188714 9500 97.42 -- 0.1248 0.123 0.1576 --
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 1.75 1.7653 -- 259 4745 0.2355 0.2833 -- 78.0
X Ray Diffraction 1.7653 1.7861 -- 277 5608 0.2234 0.2851 -- 92.0
X Ray Diffraction 1.7861 1.8079 -- 343 6080 0.1966 0.2369 -- 99.0
X Ray Diffraction 1.8079 1.8307 -- 322 6072 0.1795 0.252 -- 99.0
X Ray Diffraction 1.8307 1.8548 -- 341 6053 0.1662 0.214 -- 99.0
X Ray Diffraction 1.8548 1.8802 -- 311 6036 0.166 0.2175 -- 99.0
X Ray Diffraction 1.8802 1.9071 -- 338 6073 0.1608 0.2078 -- 99.0
X Ray Diffraction 1.9071 1.9356 -- 309 6109 0.1546 0.1806 -- 99.0
X Ray Diffraction 1.9356 1.9658 -- 302 5993 0.1453 0.1982 -- 99.0
X Ray Diffraction 1.9658 1.998 -- 315 5973 0.1435 0.1768 -- 98.0
X Ray Diffraction 1.998 2.0325 -- 312 5922 0.1387 0.1763 -- 97.0
X Ray Diffraction 2.0325 2.0695 -- 306 5769 0.1389 0.1939 -- 94.0
X Ray Diffraction 2.0695 2.1093 -- 300 6063 0.124 0.1782 -- 99.0
X Ray Diffraction 2.1093 2.1523 -- 327 6048 0.1113 0.1607 -- 99.0
X Ray Diffraction 2.1523 2.1991 -- 332 6052 0.1081 0.1389 -- 99.0
X Ray Diffraction 2.1991 2.2503 -- 333 6072 0.1059 0.1516 -- 99.0
X Ray Diffraction 2.2503 2.3066 -- 322 6058 0.1042 0.1494 -- 99.0
X Ray Diffraction 2.3066 2.3689 -- 366 6019 0.1024 0.1517 -- 99.0
X Ray Diffraction 2.3689 2.4386 -- 284 5949 0.1048 0.1571 -- 97.0
X Ray Diffraction 2.4386 2.5173 -- 307 5766 0.1058 0.152 -- 94.0
X Ray Diffraction 2.5173 2.6073 -- 316 6117 0.1117 0.1512 -- 99.0
X Ray Diffraction 2.6073 2.7117 -- 323 6103 0.1143 0.1426 -- 99.0
X Ray Diffraction 2.7117 2.8351 -- 312 6111 0.1203 0.1635 -- 99.0
X Ray Diffraction 2.8351 2.9845 -- 343 6060 0.1235 0.1648 -- 99.0
X Ray Diffraction 2.9845 3.1715 -- 320 6011 0.1215 0.1533 -- 98.0
X Ray Diffraction 3.1715 3.4163 -- 314 5916 0.1119 0.1362 -- 96.0
X Ray Diffraction 3.4163 3.76 -- 321 6124 0.1059 0.1374 -- 99.0
X Ray Diffraction 3.76 4.3038 -- 321 6125 0.1041 0.1258 -- 99.0
X Ray Diffraction 4.3038 5.4212 -- 332 5976 0.1017 0.1183 -- 97.0
X Ray Diffraction 5.4212 48.5848 -- 292 6211 0.1613 0.1804 -- 98.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 26.8421
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.005
f_chiral_restr 0.074
f_dihedral_angle_d 12.756
f_angle_d 1.164
f_bond_d 0.009
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 7740
Nucleic Acid Atoms 0
Heterogen Atoms 162
Solvent Atoms 1533

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
HKL Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: 1.8.1_1168) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
Phaser molecular replacement