X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8.5
Temperature 289.0
Details 0.7 M Sodium citrate tribasic dihydrate, 0.1 M Tris pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 113.49 α = 90
b = 113.49 β = 90
c = 158.13 γ = 120
Symmetry
Space Group H 3 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 225 mm CCD beryllium lens 2012-11-10
Diffraction Radiation
Monochromator Protocol
C(111) diamond laue monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F

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
2.25 50 100.0 0.079 -- -- 8.9 18866 18866 0.0 -3.0 --
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)
2.25 2.29 100.0 0.742 -- 2.1 8.5 --

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 2.25 41.77 0.0 0.0 17890 17890 969 99.97 0.18828 0.18828 0.18571 0.23836 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 2.25 2.308 -- 70 1317 0.256 0.33 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 49.73
Anisotropic B[1][1] -2.36
Anisotropic B[1][2] -2.36
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -2.36
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 7.66
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_other 0.001
r_gen_planes_refined 0.007
r_chiral_restr 0.088
r_dihedral_angle_4_deg 22.203
r_dihedral_angle_3_deg 16.767
r_dihedral_angle_2_deg 37.02
r_dihedral_angle_1_deg 5.772
r_angle_other_deg 0.838
r_angle_refined_deg 1.536
r_bond_other_d 0.001
r_bond_refined_d 0.014
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2615
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 110

Software

Computing
Computing Package Purpose
LS-CAT modified MD-2 Data Collection
HKL-3000 Data Reduction (intensity integration)
HKL-3000 Data Reduction (data scaling)
HKL-3000,MOLREP Structure Solution
REFMAC 5.7.0029, COOT, HKL-3000 Structure Refinement
Software
Software Name Purpose
HKL-3000 refinement
COOT refinement
REFMAC version: 5.7.0029 refinement
MOLREP model building
HKL-3000 model building
LS-CAT version: modified MD-2 data collection