X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 291.0
Details PEG 3450, Tris, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 40.67 α = 90
b = 46.27 β = 90
c = 64.74 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD BRANDEIS - B4 -- 1999-02-10
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X25 -- NSLS X25

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 94.8 0.04 0.04 -- 4.5 11260 11260 0.0 0.0 10.0
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)
1.8 1.85 99.4 0.05 0.05 29.0 4.0 966

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
MOLECULAR REPLACEMENT 1.8 30.0 0.0 0.0 11421 11421 1083 96.4 -- -- 0.219 0.232 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 -- 201 1722 0.226 0.277 0.02 99.2
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 16.5
Anisotropic B[1][1] 2.51
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -2.97
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.46
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 3.45
c_mcbond_it 1.62
c_bond_d 0.005
c_improper_angle_d 0.72
c_angle_deg 1.3
c_dihedral_angle_d 23.9
c_mcangle_it 2.01
c_scbond_it 2.72
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.22
Luzzati Sigma A (Observed) 0.03
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.23
Luzzati Sigma A (R-Free Set) 0.13
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 838
Nucleic Acid Atoms 0
Heterogen Atoms 28
Solvent Atoms 105

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
AMORE Structure Solution
CNS 0.9 Structure Refinement
Software
Software Name Purpose
SCALEPACK data reduction
AMORE model building
CNS version: 0.9 refinement
DENZO data collection