X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 277.0
Details 30% PEG400, 0.1 M MgCl2, HEPES 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 130.5 α = 90
b = 130.5 β = 90
c = 208.5 γ = 120
Symmetry
Space Group P 31 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 103
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 1998-05-01
AREA DETECTOR MARRESEARCH -- 1999-12-21
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL9-2 0.96-1.2 SSRL BL9-2
SYNCHROTRON SSRL BEAMLINE BL9-1 0.98 SSRL BL9-1
SYNCHROTRON SSRL BEAMLINE BL7-1 1.08 SSRL BL7-1
SYNCHROTRON ALS BEAMLINE 5.0.2 1.0 ALS 5.0.2

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
2.8 30 99.1 -- 0.031 -- 4.0 51328 50859 1.0 1.0 --
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)
2.8 2.9 99.1 -- 0.617 1.6 4.0 50859

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
MIR 2.8 30.0 1.0 1.0 50859 45998 2542 99.1 0.256 0.256 0.254 0.279 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 2.8 2.9 50859 2542 -- 0.241 0.251 -- 99.1
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 71.1
Anisotropic B[1][1] -4.85
Anisotropic B[1][2] 1.5
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -4.85
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 9.71
RMS Deviations
Key Refinement Restraint Deviation
c_improper_angle_d 2.33
c_dihedral_angle_d 24.7
c_bond_d 0.034
c_angle_deg 3.0
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.67
Luzzati Sigma A (Observed) 0.71
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.63
Luzzati Sigma A (R-Free Set) 0.44
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6033
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 393

Software

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