X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 298.0
Details PEG 400, MgCl2, pH 7.0, temperature 298K, VAPOR DIFFUSION, HANGING DROP

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 121.7 α = 90
b = 132.5 β = 90
c = 179.1 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC CCD300 -- 2010-01-27
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON CLSI BEAMLINE 08ID-1 0.97949 CLSI 08ID-1

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
3.92 48.8 81.8 -- -- -- 7.4 21818 21818 0.0 0.0 --
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)
3.92 4.02 24.9 -- -- 2.2 7.5 466

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 3.92 48.79 -- 0.0 21818 21818 1096 82.07 0.2996 0.2996 0.2971 0.3512 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 3.922 4.023 466 20 459 0.411 0.411 -- 24.95
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 145.236
Anisotropic B[1][1] 0.01
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.0
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.01
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 4.027
r_scbond_it 2.034
r_mcangle_it 2.216
r_mcbond_other 0.102
r_bond_refined_d 0.011
r_bond_other_d 0.002
r_angle_refined_deg 1.235
r_angle_other_deg 0.834
r_dihedral_angle_1_deg 6.364
r_dihedral_angle_2_deg 38.315
r_dihedral_angle_3_deg 18.431
r_dihedral_angle_4_deg 12.729
r_chiral_restr 0.061
r_gen_planes_refined 0.005
r_gen_planes_other 0.001
r_mcbond_it 1.172
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 12965
Nucleic Acid Atoms 0
Heterogen Atoms 14
Solvent Atoms 0

Software

Computing
Computing Package Purpose
MxDC Data Collection
XDS Data Reduction (intensity integration)
XSCALE Data Reduction (data scaling)
PHASER Structure Solution
REFMAC 5.5.0102 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.10 data extraction
REFMAC5 refinement
Phaser molecular replacement
HKL data reduction