X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 7.5
Temperature 291.0
Details 40% PEG 1000, 0.1M potassium nitrate, 0.1M HEPES, pH7.5, Microbatch crystallization under oil, 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 52.11 α = 90
b = 43.59 β = 93.1
c = 69.94 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 210 -- 2012-08-08
Diffraction Radiation
Monochromator Protocol
Si 111 CHANNEL SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X4A 0.97904 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
2.38 50 99.5 0.138 -- -- 2.2 24545 24422 0.0 0.0 32.67
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)
2.4 2.49 99.8 0.568 -- 1.4 2.2 2465

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 2.377 42.852 -- 1.2 -- 24390 1189 98.42 -- 0.2 0.199 0.235 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 2.377 2.485 -- 128 2731 0.287 0.342 -- 92.0
X Ray Diffraction 2.485 2.616 -- 204 2883 0.266 0.304 -- 100.0
X Ray Diffraction 2.616 2.78 -- 142 2935 0.253 0.3 -- 100.0
X Ray Diffraction 2.78 2.994 -- 133 2931 0.228 0.276 -- 99.0
X Ray Diffraction 2.994 3.295 -- 165 2925 0.223 0.259 -- 99.0
X Ray Diffraction 3.295 3.772 -- 145 2921 0.189 0.243 -- 99.0
X Ray Diffraction 3.772 4.751 -- 146 2929 0.148 0.169 -- 99.0
X Ray Diffraction 4.751 42.859 -- 126 2946 0.169 0.176 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 39.547
Anisotropic B[1][1] 3.403
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -2.739
Anisotropic B[2][2] -0.649
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.754
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 16.632
f_plane_restr 0.006
f_chiral_restr 0.096
f_angle_d 1.411
f_bond_d 0.009
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2459
Nucleic Acid Atoms 0
Heterogen Atoms 4
Solvent Atoms 48

Software

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