X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.6
Temperature 293.0
Details Tris, HCl, HEPES, lithium sulphate, pH 7.6, VAPOR DIFFUSION, HANGING DROP at 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 64.72 α = 90
b = 64.72 β = 90
c = 69.57 γ = 120
Symmetry
Space Group P 31 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MARRESEARCH -- 2000-04-14
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X31 1.100 EMBL/DESY, HAMBURG X31

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 29.6 100.0 0.06 -- -- 9.5 11799 11799 -- -- 28.5
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)
2.0 2.02 99.5 0.306 -- 5.8 7.9 390

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 2.0 29.0 -- 0.0 11799 11760 559 100.0 0.155 0.155 0.154 0.212 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 2.0 2.02 390 -- -- -- -- -- 99.5
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model anisotropic
Mean Isotropic B 25.813
Anisotropic B[1][1] 2.09
Anisotropic B[1][2] 1.05
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 2.09
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -3.14
RMS Deviations
Key Refinement Restraint Deviation
r_rigid_bond_restr 1.954
r_sphericity_bonded 4.616
r_bond_refined_d 0.021
p_chiral_restr 0.105
p_plane_restr 0.008
p_scangle_it 5.842
p_scbond_it 3.836
p_mcangle_it 2.56
p_mcbond_it 1.642
p_hb_or_metal_coord 0.171
p_angle_d 1.831
p_angle_deg 1.831
p_bond_d 0.021
r_bond_other_d 0.001
r_angle_refined_deg 1.831
r_angle_other_deg 0.824
r_dihedral_angle_1_deg 5.479
r_chiral_restr 0.105
r_gen_planes_refined 0.008
r_gen_planes_other 0.003
r_mcbond_it 1.642
r_mcangle_it 2.56
r_scbond_it 3.836
r_scangle_it 5.842
r_sphericity_free 14.373
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 782
Nucleic Acid Atoms 0
Heterogen Atoms 1
Solvent Atoms 145

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
AMORE Structure Solution
REFMAC Structure Refinement
Software
Software Name Purpose
REFMAC refinement
AMoRE model building
SCALEPACK data reduction
DENZO data collection