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 0.2 M lithium sulfate, 0.1 M Tris-HCl, 30% PEG 4000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 87.69 α = 90
b = 121.99 β = 90
c = 153.3 γ = 90
Symmetry
Space Group F 2 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 210r -- 2012-10-04
Diffraction Radiation
Monochromator Protocol
double crystal monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-BM 0.9792 APS 19-BM

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
1.64 35.9 99.4 0.087 -- -- 7.4 49631 49631 0.0 0.0 32.5
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)
1.64 1.67 96.7 0.605 -- 2.1 4.8 2403

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 1.64 36.0 0.0 0.0 49630 49630 2509 98.87 0.1298 0.1298 0.1277 0.1686 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 1.641 1.683 3205 170 3035 0.301 0.405 -- 90.38
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 29.3068
Anisotropic B[1][1] 0.1
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.36
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.47
RMS Deviations
Key Refinement Restraint Deviation
r_sphericity_bonded 18.496
r_sphericity_free 35.649
r_bond_refined_d 0.014
r_bond_other_d 0.001
r_angle_refined_deg 1.46
r_angle_other_deg 0.98
r_dihedral_angle_1_deg 5.488
r_dihedral_angle_2_deg 38.596
r_dihedral_angle_3_deg 14.135
r_dihedral_angle_4_deg 16.996
r_chiral_restr 0.104
r_gen_planes_refined 0.008
r_gen_planes_other 0.001
r_rigid_bond_restr 3.819
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2237
Nucleic Acid Atoms 0
Heterogen Atoms 4
Solvent Atoms 316

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