X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4.5
Temperature 293.0
Details 200 mM magnesium sulfate, 5.3% PEG 3350, and 100 mM acetate pH 4.5

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 94.35 α = 90
b = 94.35 β = 90
c = 50.72 γ = 90
Symmetry
Space Group P 4 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV -- 2012-04-24
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RUH3R 1.5418 -- --

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
2.4 20 99.3 -- 0.068 -- 4.7 -- 9374 -- -- --
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 98.3 0.434 -- 2.8 3.8 --

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 2.4 20.0 -- 0.0 -- 8777 927 93.5 -- -- 0.2117 0.2523 Random selection
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 2.4 2.49 -- 78 714 0.3084 0.3639 -- 86.3
X Ray Diffraction 2.49 2.58 -- 77 711 0.2953 0.3313 -- 87.7
X Ray Diffraction 2.58 2.7 -- 83 766 0.2631 0.368 -- 90.6
X Ray Diffraction 2.7 2.84 -- 83 773 0.2535 0.2962 -- 93.4
X Ray Diffraction 2.84 3.02 -- 101 763 0.2379 0.3047 -- 93.6
X Ray Diffraction 3.02 3.25 -- 91 809 0.2176 0.2602 -- 96.5
X Ray Diffraction 3.25 3.58 -- 92 795 0.2189 0.2364 -- 95.6
X Ray Diffraction 3.58 4.09 -- 111 808 0.1865 0.2263 -- 96.7
X Ray Diffraction 4.09 5.14 -- 103 842 0.1696 0.2209 -- 97.9
X Ray Diffraction 5.14 20.0 -- 108 869 0.2019 0.2278 -- 95.5
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 42.0072
Anisotropic B[1][1] -8.591
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -8.591
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 17.182
RMS Deviations
Key Refinement Restraint Deviation
c_bond_d 0.007
c_mcangle_it 2.393
c_scangle_it 3.129
c_scbond_it 2.082
c_mcbond_it 1.421
c_angle_d 1.491
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1268
Nucleic Acid Atoms 0
Heterogen Atoms 104
Solvent Atoms 0

Software

Software
Software Name Purpose
HKL-2000 data scaling
PHASER phasing
CNS refinement
PDB_EXTRACT data extraction version: 3.20
HKL-2000 data reduction