X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 298.0
Details 15% PEG 4000, 100MM HEPES, 100MM NACL, 50MM MGCL2, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 82.4 α = 90
b = 82.4 β = 90
c = 199.7 γ = 120
Symmetry
Space Group P 31 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 138
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD BRANDEIS -- 1999-06-19
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
2.4 30 98.0 0.085 -- -- 8.0 -- 27877 -- 2.0 34.4
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)
2.5 2.59 100.0 0.21 -- -- 8.0 --

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
-- 2.5 10.0 0.0 0.0 26809 26809 2495 97.8 0.26 0.25 0.25 0.29 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 2.5 2.65 -- 220 4126 0.323 0.413 0.028 96.1
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 44.2
Anisotropic B[1][1] 0.25
Anisotropic B[1][2] -0.79
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.25
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.51
RMS Deviations
Key Refinement Restraint Deviation
c_improper_angle_d 1.01
c_bond_d 0.01
c_angle_deg 1.6
c_dihedral_angle_d 21.7
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.37
Luzzati Sigma A (Observed) 0.33
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.5
Luzzati Sigma A (R-Free Set) 0.43
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4398
Nucleic Acid Atoms 1036
Heterogen Atoms 2
Solvent Atoms 207

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
CNS Structure Solution
CNS 0.5 Structure Refinement
Software
Software Name Purpose
CNS version: 0.5 refinement
CNS model building