X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 298.0
Details 0.1 M Hepes (pH 7.5), 1 M succinic Acid, 1% (w/v) PEG MME 2000, temperature 298K, VAPOR DIFFUSION, HANGING DROP

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 119.04 α = 90
b = 121.22 β = 90
c = 122.88 γ = 90
Symmetry
Space Group I 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RIGAKU SATURN 944+ -- 2009
Diffraction Radiation
Monochromator Protocol
VARIMAX SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
rotating anode Cu Ka 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
2.8 20 100.0 0.152 -- -- 7.2 -- 22155 -- -- --
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)
2.8 2.85 99.5 0.555 -- -- 6.2 1094

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 2.8 19.84 -- 0.0 -- 22139 1127 99.83 -- 0.1904 0.1867 0.2582 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 2.801 2.872 -- 85 1487 0.287 0.414 -- 98.43
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 21.8225
Anisotropic B[1][1] 2.18
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.85
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.33
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 4.01
r_scbond_it 2.333
r_mcangle_it 1.443
r_mcbond_it 0.729
r_gen_planes_refined 0.008
r_chiral_restr 0.112
r_dihedral_angle_4_deg 20.19
r_dihedral_angle_3_deg 18.267
r_dihedral_angle_2_deg 33.962
r_dihedral_angle_1_deg 10.15
r_angle_refined_deg 1.73
r_bond_refined_d 0.017
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4029
Nucleic Acid Atoms 0
Heterogen Atoms 14
Solvent Atoms 154

Software

Computing
Computing Package Purpose
SCALEPACK Data Reduction (data scaling)
SHARP Structure Solution
REFMAC 5.5.0072 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.10 data extraction
REFMAC5 version: 5.5.0072 refinement
SCALEPACK data reduction