X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.3
Temperature 290.0
Details 60.8% MPD, 100MM NAHEPES PH 7.3- 7.4, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 47.46 α = 90
b = 58.63 β = 90
c = 62.39 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 ADSC QUANTUM 315r -- 2011-08-01
Diffraction Radiation
Monochromator Protocol
double crystal, Si 111 SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-ID 0.9791750 APS 19-ID

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
1.95 50 99.7 0.088 -- -- 8.6 -- 13168 0.0 -3.0 28.96
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)
1.95 2.0 95.7 0.484 0.484 3.05 3.8 961

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
SAD 1.95 42.73 -- 0.0 13214 13167 649 -- 0.177 0.177 0.176 0.207 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 1.95 2.0 -- 50 782 0.255 0.297 -- 95.19
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model isotropic, TLS
Mean Isotropic B 24.86
Anisotropic B[1][1] 0.73
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.35
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.38
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_other 0.001
r_gen_planes_refined 0.006
r_chiral_restr 0.082
r_dihedral_angle_4_deg 20.953
r_dihedral_angle_3_deg 12.647
r_dihedral_angle_2_deg 40.147
r_dihedral_angle_1_deg 6.053
r_angle_other_deg 0.885
r_angle_refined_deg 1.455
r_bond_other_d 0.001
r_bond_refined_d 0.013
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1152
Nucleic Acid Atoms 0
Heterogen Atoms 17
Solvent Atoms 117

Software

Computing
Computing Package Purpose
BluIce 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
REFMAC version: 5.6.0117 refinement
PHASER model building
BluIce data collection