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, 1.26 M Ammonium sulfate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 45.92 α = 90
b = 152.39 β = 103.12
c = 100.24 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r -- 2012-12-16
Diffraction Radiation
Monochromator Protocol
Si(111) double crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-ID 0.97940 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 50 99.7 0.074 -- -- 3.7 91010 90011 -- -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)
2.0 2.07 98.6 0.17 -- 7.0 3.3 8840

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 2.0 38.6 -- 0.0 89975 89975 4514 99.56 0.1481 0.1481 0.1455 0.1952 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 1.999 2.051 6392 292 6100 0.138 0.208 -- 96.92
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 17.5895
Anisotropic B[1][1] 0.41
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.15
Anisotropic B[2][2] -0.37
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.07
RMS Deviations
Key Refinement Restraint Deviation
r_sphericity_bonded 6.474
r_sphericity_free 29.672
r_bond_refined_d 0.007
r_bond_other_d 0.001
r_angle_refined_deg 1.111
r_angle_other_deg 0.718
r_dihedral_angle_1_deg 5.903
r_dihedral_angle_2_deg 39.141
r_dihedral_angle_3_deg 12.528
r_dihedral_angle_4_deg 15.46
r_chiral_restr 0.07
r_gen_planes_refined 0.004
r_gen_planes_other 0.001
r_rigid_bond_restr 2.677
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 9753
Nucleic Acid Atoms 0
Heterogen Atoms 5
Solvent Atoms 904

Software

Computing
Computing Package Purpose
SBC COLLECT Data Collection
HKL-3000 Data Reduction (intensity integration)
HKL-3000 Data Reduction (data scaling)
HKL-3000, MLPHARE, DM, SHELXDE, ARP/WARP, RESOLVE, COOT Structure Solution
REFMAC 5.7.0029 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
REFMAC5 version: 5.7.0029 refinement