X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Microbatch Crystallization Under Oil
pH 7.5
Temperature 277.0
Details 40% PEG 400, 0.1M lithium sulfate, 0.1M HEPES, pH 7.5, Microbatch crystallization under oil, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 69 α = 90
b = 30.46 β = 92.68
c = 70.06 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 ADSC QUANTUM 4 -- 2012-10-11
Diffraction Radiation
Monochromator Protocol
Si 111 CHANNEL SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X4A 0.97905 NSLS X4A

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
2.43 50 97.9 0.094 -- -- 2.4 21255 20809 0.0 0.0 31.32
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)
2.43 2.52 95.1 0.212 -- 4.34 2.3 2149

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
MIR 2.433 34.992 -- 1.34 -- 20800 990 97.25 -- 0.199 0.197 0.227 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 2.433 2.562 -- 132 2658 0.259 0.29 -- 91.0
X Ray Diffraction 2.562 2.722 -- 166 2867 0.226 0.294 -- 99.0
X Ray Diffraction 2.722 2.932 -- 137 2839 0.214 0.278 -- 99.0
X Ray Diffraction 2.932 3.227 -- 142 2849 0.207 0.302 -- 98.0
X Ray Diffraction 3.227 3.693 -- 133 2879 0.19 0.203 -- 98.0
X Ray Diffraction 3.693 4.652 -- 149 2828 0.181 0.188 -- 98.0
X Ray Diffraction 4.652 34.996 -- 131 2890 0.179 0.19 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 41.067
Anisotropic B[1][1] -6.83
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -7.366
Anisotropic B[2][2] -1.56
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 8.39
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 14.339
f_plane_restr 0.005
f_chiral_restr 0.087
f_angle_d 1.169
f_bond_d 0.006
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2442
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 81

Software

Computing
Computing Package Purpose
ADSC Quantum Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
BALBES Structure Solution
PHENIX (phenix.refine: 1.7.2_869) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.100 data extraction
phenix refinement