X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8
Temperature 281.0
Details 0.1M TRIS-CL, pH 8.0; 18% PEG 4000; 0.2M CALCIUM CHLORIDE; 3% DMSO, VAPOR DIFFUSION HANGING DROP, temperature 281K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 77.22 α = 90
b = 77.22 β = 90
c = 222.05 γ = 120
Symmetry
Space Group P 61 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 17-ID 1.0 APS 17-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
1.8 50 99.2 0.056 -- -- -- -- 38811 -- -- --
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)
1.8 1.83 99.5 0.656 -- -- -- 1813

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
-- 1.8 50.0 -- 0.0 -- 38811 1818 98.95 -- 0.201 0.199 0.235 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 1.8 1.91 -- 272 5494 0.241 0.28 -- 98.95
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 43.6
Anisotropic B[1][1] -5.975
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -5.975
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 11.95
RMS Deviations
Key Refinement Restraint Deviation
t_nbd 0.042
t_it 1.856
t_gen_planes 0.017
t_trig_c_planes 0.01
t_dihedral_angle_d 19.952
t_angle_deg 1.175
t_bond_d 0.01
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2438
Nucleic Acid Atoms 0
Heterogen Atoms 60
Solvent Atoms 184

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
BUSTER-TNT 2.1.1 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.004 data extraction
TNT refinement
SCALEPACK data scaling
DENZO collection/data indexing