X-RAY DIFFRACTION Experimental Data & Validation


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Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.5
Temperature 277.0
Details 0.1M Tris, 12% PEG8000, 0.05M MgCl2, 0.15M NaCl, 5% Ethylene glycol, 1mM TCEP, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 197 α = 90
b = 197 β = 90
c = 50.18 γ = 120
Symmetry
Space Group H 3

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 300 mm CCD -- 2010-07-15
Diffraction Radiation
Monochromator Protocol
Double crystal cryo-cooled Si (111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 23-ID-B 1.033 APS 23-ID-B

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
2.99 20 98.8 0.088 -- -- 5.8 14671 14501 0.0 -3.0 103.571
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)
2.99 3.07 100.0 0.928 -- 2.13 -- --

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 2.99 19.8 -- 0.0 14671 14499 1444 98.83 0.2182 0.2182 0.2137 0.2594 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 2.99 3.066 -- 106 938 0.291 0.375 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 113.981
Anisotropic B[1][1] -2.21
Anisotropic B[1][2] -1.11
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -2.21
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 3.32
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_refined 0.004
r_chiral_restr 0.074
r_dihedral_angle_4_deg 9.986
r_dihedral_angle_3_deg 18.176
r_dihedral_angle_2_deg 35.737
r_dihedral_angle_1_deg 5.874
r_angle_refined_deg 1.16
r_bond_refined_d 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3323
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 1

Software

Computing
Computing Package Purpose
JBlu-Ice Data Collection
XDS Data Reduction (intensity integration)
XSCALE Data Reduction (data scaling)
Phaser Structure Solution
REFMAC 5.6.0117 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
REFMAC5 refinement
Xscale data reduction