X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7
Temperature 293.0
Details PEG 2000, Bis-Tris buffer, nonyl-beta-D-glucoside, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 112.11 α = 90
b = 112.11 β = 90
c = 161.41 γ = 90
Symmetry
Space Group P 43 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARRESEARCH -- --
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON MPG/DESY, HAMBURG BEAMLINE BW6 -- MPG/DESY, HAMBURG BW6

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
2.4 20 99.6 0.043 -- -- -- 39379 39379 0.0 0.0 46.3
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)
2.4 2.49 100.0 0.147 -- -- -- 7703

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
THE STRUCTURE WAS SOLVED BY MULTIPLE ANOMALOUS DISPERSION (MAD) USING 5 DIFFERENT WAVELENGTH (2X FE-EDGE + 2X CU-EDGE + 1 REMOTE). THE DATA STATISTICS GIVEN CORRESPOND TO THE REFERENCE WAVELENGTH WHICH WAS USED FOR REFINEMENT. THE STRUCTURE WAS SOLVED WITH SHARP. 2.4 20.0 0.0 0.0 -- 39379 1972 96.3 -- 0.222 0.222 0.264 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 2.4 2.49 -- 198 3623 0.254 0.299 0.021 95.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 50.6
Anisotropic B[1][1] 9.46
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 9.46
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -18.92
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 5.41
c_scbond_it 4.43
c_mcangle_it 4.37
c_mcbond_it 3.1
c_improper_angle_d 1.09
c_bond_d 0.008
c_angle_deg 1.6
c_dihedral_angle_d 19.7
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.28
Luzzati Sigma A (Observed) 0.2
Luzzati Resolution Cutoff (Low) 4.0
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5851
Nucleic Acid Atoms 0
Heterogen Atoms 174
Solvent Atoms 119

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
SHARP Structure Solution
CNS 0.3 Structure Refinement
Software
Software Name Purpose
CNS version: 0.3 refinement
SHARP model building