X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 293.0
Details PROTEIN: 10 MG/ML in 0.01M HEPES pH 7.0, 0.3 M NaCl, 0.001 M DTT; RESERVOIR: 0.1M BICINE pH9.0, 0.2 M sodium phosphate dibasic, 18% PEG 3350, vapor diffusion, hanging drop, temperature 293K, VAPOR DIFFUSION, HANGING DROP

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 136.6 α = 90
b = 58.4 β = 130.04
c = 91.8 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2009-11-06
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 5.0.2 1.0092 ALS 5.0.2

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
2.88 50 98.6 0.056 -- -- 4.4 -- 12548 -- -- --
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)
2.9 3.0 92.4 0.541 -- -- 3.7 1174

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 2.875 36.224 -- 1.34 -- 12465 1263 97.41 -- 0.2186 0.2146 0.254 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 2.8753 2.9903 -- 126 1081 0.3301 0.4281 -- 86.0
X Ray Diffraction 2.9903 3.1264 -- 136 1222 0.304 0.3126 -- 97.0
X Ray Diffraction 3.1264 3.2911 -- 141 1257 0.2506 0.2864 -- 98.0
X Ray Diffraction 3.2911 3.4971 -- 133 1253 0.2514 0.2919 -- 99.0
X Ray Diffraction 3.4971 3.7669 -- 145 1258 0.2354 0.3062 -- 99.0
X Ray Diffraction 3.7669 4.1455 -- 141 1269 0.2207 0.262 -- 99.0
X Ray Diffraction 4.1455 4.7442 -- 142 1267 0.1802 0.2081 -- 100.0
X Ray Diffraction 4.7442 5.9729 -- 148 1287 0.203 0.2265 -- 100.0
X Ray Diffraction 5.9729 36.2267 -- 151 1308 0.2006 0.245 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 138.769
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 9.914
f_plane_restr 0.003
f_chiral_restr 0.037
f_angle_d 0.51
f_bond_d 0.006
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3226
Nucleic Acid Atoms 0
Heterogen Atoms 1
Solvent Atoms 0

Software

Computing
Computing Package Purpose
HKL Data Reduction (intensity integration)
HKL Data Reduction (data scaling)
PHENIX (phenix.refine: 1.8_1069) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
HKL data reduction