X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 293.0
Details 100 mM MES, pH 6.5, 19-24% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 65.13 α = 90
b = 74.31 β = 90
c = 77.75 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 90
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD PSI PILATUS 6M Dynamical bendable mirrors 2011-06-22
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SLS BEAMLINE X10SA 1.00000 SLS X10SA

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
2.2 45 99.8 0.033 -- -- 6.18 20076 20045 -- -3.0 53.958
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)
2.2 2.3 100.0 0.165 -- 9.84 -- --

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 2.5 45.0 -- 0.0 20076 20045 956 99.8 -- 0.2337 0.2266 0.3174 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 2.5 2.565 -- 77 886 0.33 0.58 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 40.3721
Anisotropic B[1][1] -0.91
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.8
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.71
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 3.133
r_scbond_it 1.873
r_mcangle_it 1.497
r_mcbond_it 0.786
r_gen_planes_refined 0.007
r_chiral_restr 0.099
r_dihedral_angle_4_deg 17.039
r_dihedral_angle_3_deg 21.248
r_dihedral_angle_2_deg 36.121
r_dihedral_angle_1_deg 6.398
r_angle_refined_deg 1.531
r_bond_refined_d 0.014
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2699
Nucleic Acid Atoms 0
Heterogen Atoms 35
Solvent Atoms 19

Software

Computing
Computing Package Purpose
XDS Data Collection
XSCALE Data Reduction (intensity integration)
XSCALE Data Reduction (data scaling)
PHASER Structure Solution
REFMAC 5.5.0070 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.10 data extraction
REFMAC5 refinement
Phaser version: 1.3.3 molecular replacement
Xscale data reduction