X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 6
Temperature 277.0
Details K/Na tartrate, sodium thiocynate, glycerol, pH 6.0, vapor diffusion, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 72.8 α = 90
b = 85.63 β = 90
c = 92.98 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
2 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL PSI PILATUS 6M Meridionally-bent fused silica mirror 2011-07-22
CCD ADSC QUANTUM -- 2009-06-04
Diffraction Radiation
Monochromator Protocol
Double silicon(111) crystal Single Wavelength
Double silicon(111) crystal Single Wavelength
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X25 1.1 NSLS X25
SYNCHROTRON NSLS BEAMLINE X25 0.9792 NSLS X25

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
2.69 50 99.9 0.069 -- -- 8.5 16922 16446 2.0 2.0 77.2
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)
2.695 2.75 99.9 0.463 -- -- 8.1 815

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
SAD 2.6951 47.633 -- 0.0 16370 15941 1157 95.92 0.2317 0.2317 0.2278 0.2838 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 2.6951 2.8177 1530 119 -- 0.42 0.5162 -- --
X Ray Diffraction 2.8177 2.9622 1781 141 -- 0.295 0.3803 -- --
X Ray Diffraction 2.9622 3.152 1801 153 -- 0.2615 0.339 -- --
X Ray Diffraction 3.152 3.3953 1868 136 -- 0.2514 0.3059 -- --
X Ray Diffraction 3.3953 3.7369 1892 165 -- 0.2329 0.2927 -- --
X Ray Diffraction 3.7369 4.2774 1914 154 -- 0.1996 0.2492 -- --
X Ray Diffraction 4.2774 5.3878 1941 149 -- 0.1844 0.2187 -- --
X Ray Diffraction 5.3878 47.6399 2057 144 -- 0.2206 0.2872 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 75.6584
Anisotropic B[1][1] 20.0033
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 11.3694
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -31.3727
RMS Deviations
Key Refinement Restraint Deviation
flanairty 0.001
fhirality 0.041
f_dihedral_angle_d 16.731
f_bond_d 0.1
f_angle_deg 0.6
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2749
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 0

Software

Computing
Computing Package Purpose
CBASS Data Collection
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
SHELXD Structure Solution
PHENIX (phenix.refine: 1.6.2_432) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.10 data extraction
REFMAC5 refinement
SHELX phasing
SCALEPACK data reduction
DENZO data collection