X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.8
Temperature 298.0
Details Well solution: 200 mM Sodium Citrate (pH 5.8),11% (W/V) PEG 4000; protein solution: 20 mM Tris-Cl (pH 7.0),50 mM NaCl, 5mM beta-mercaptoethanol, Vapor Diffusion, Hanging Drop, Temperature 298K, VAPOR DIFFUSION, HANGING DROP

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 51.49 α = 90
b = 66.21 β = 90
c = 72.13 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 NOIR-1 -- 2008-04-30
Diffraction Radiation
Monochromator Protocol
Double crystal MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 4.2.2 0.9792, 0.9795, 0.9643 ALS 4.2.2

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
1.4 41.91 99.7 0.061 -- -- 6.65 47946 47946 0.0 0.0 22.0
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)
1.4 1.45 98.8 0.441 -- 2.4 4.91 4615

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
MAD 1.4 5.0 -- 0.0 47946 47946 4829 100.0 0.20159 0.20159 0.19766 0.23647 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 1.4 1.433 2912 340 2912 0.285 0.315 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 14.0
Anisotropic B[1][1] -0.97
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.19
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.22
RMS Deviations
Key Refinement Restraint Deviation
r_sphericity_bonded 4.098
r_sphericity_free 8.379
r_rigid_bond_restr 2.497
r_nbd_refined 0.238
r_gen_planes_other 0.001
r_gen_planes_refined 0.007
r_chiral_restr 0.101
r_dihedral_angle_4_deg 20.213
r_dihedral_angle_3_deg 13.038
r_dihedral_angle_2_deg 33.178
r_dihedral_angle_1_deg 4.919
r_angle_other_deg 0.954
r_angle_refined_deg 1.584
r_bond_other_d 0.001
r_bond_refined_d 0.016
r_nbd_other 0.188
r_nbtor_refined 0.182
r_nbtor_other 0.085
r_xyhbond_nbd_refined 0.14
r_symmetry_vdw_refined 0.099
r_symmetry_vdw_other 0.27
r_symmetry_hbond_refined 0.185
r_mcbond_it 1.876
r_mcbond_other 0.71
r_mcangle_it 2.317
r_scbond_it 3.759
r_scangle_it 4.96
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1938
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 205

Software

Computing
Computing Package Purpose
CrystalClear Data Collection
d*TREK Data Reduction (intensity integration)
d*TREK Data Reduction (data scaling)
Solve/Resolve Structure Solution
REFMAC 5.2.0019 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.2.0019 refinement
SOLVE/RESOLVE model building
CrystalClear data collection