X-RAY DIFFRACTION Experimental Data & Validation


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Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5
Temperature 289.0
Details 1 M sodium/potassium phosphate, 0.01 M IMP, 0.01 M mycophenolic acid, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 111.96 α = 90
b = 111.96 β = 90
c = 188.99 γ = 90
Symmetry
Space Group I 4 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r -- 2012-06-04
Diffraction Radiation
Monochromator Protocol
double crystal monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-ID 0.9792 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
2.24 30.6 99.9 0.09 -- -- 21.7 29245 29245 0.0 0.0 56.9
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)
2.24 2.28 100.0 0.913 -- 5.48 22.1 1424

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 2.24 30.7 0.0 0.0 29244 29244 1541 99.78 0.1918 0.1918 0.1896 0.2319 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 2.239 2.297 1938 99 1839 0.209 0.262 -- 99.9
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 67.5131
Anisotropic B[1][1] 0.14
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.14
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.28
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_refined 0.007
r_chiral_restr 0.111
r_dihedral_angle_4_deg 19.59
r_dihedral_angle_3_deg 19.179
r_dihedral_angle_2_deg 38.823
r_dihedral_angle_1_deg 6.775
r_angle_refined_deg 1.74
r_bond_refined_d 0.015
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3474
Nucleic Acid Atoms 0
Heterogen Atoms 47
Solvent Atoms 87

Software

Computing
Computing Package Purpose
SBC-collect Data Collection
HKL-3000 Data Reduction (intensity integration)
HKL-3000 Data Reduction (data scaling)
PHENIX Structure Solution
REFMAC 5.6.0117 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
REFMAC5 version: 5.6.0117 refinement
HKL data reduction