X-RAY DIFFRACTION Experimental Data & Validation


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Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8.5
Temperature 289.0
Details 2 M ammonium sulfate, 0.1 M Tris-HCl, 0.1 M sodium malonate , pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 39.99 α = 90
b = 55.81 β = 90
c = 104.7 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 -- 2012-11-02
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
1.3 32.5 97.6 0.066 -- -- 4.7 57044 57044 0.0 0.0 18.3
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)
1.3 1.32 75.6 0.379 -- 2.23 2.2 2162

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 1.3 32.5 0.0 0.0 56966 56966 2890 97.55 0.1295 0.1295 0.1281 0.1556 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 1.301 1.335 3138 147 2991 0.233 0.254 -- 76.7
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 17.1247
Anisotropic B[1][1] 0.99
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.61
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.38
RMS Deviations
Key Refinement Restraint Deviation
r_sphericity_bonded 10.253
r_sphericity_free 31.622
r_bond_refined_d 0.013
r_bond_other_d 0.001
r_angle_refined_deg 1.638
r_angle_other_deg 0.965
r_dihedral_angle_1_deg 5.749
r_dihedral_angle_2_deg 32.431
r_dihedral_angle_3_deg 12.764
r_dihedral_angle_4_deg 18.962
r_chiral_restr 0.091
r_gen_planes_refined 0.009
r_gen_planes_other 0.001
r_rigid_bond_restr 3.098
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1891
Nucleic Acid Atoms 0
Heterogen Atoms 25
Solvent Atoms 338

Software

Computing
Computing Package Purpose
SBC-collect Data Collection
HKL-3000 Data Reduction (intensity integration)
HKL-3000 Data Reduction (data scaling)
SHELXD, MLPHARE, DM, SOLVE/RESOLVE, HKL-3000 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