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 1 mM DTT, 60 mM HEPES, 120 mM CaCl2, 16.8% PEG400, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 56.9 α = 94.87
b = 62.48 β = 110.45
c = 65.5 γ = 99.17
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 298
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD NOIR-1 Rosenbaum-Rock monochromator 1: high-resolution double-crystal sagittal focusing, Rosenbaum-Rock monochromator 2: double crystal, Rosenbaum-Rock vertical focusing mirror 2005-06-09
Diffraction Radiation
Monochromator Protocol
Rosenbaum-Rock monochromator 1: high-resolution double-crystal sagittal focusing, Rosenbaum-Rock monochromator 2: double crystal, Rosenbaum-Rock vertical focusing mirror SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 4.2.2 1.127 ALS 4.2.2

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 40 96.7 0.088 0.088 -- 1.96 55752 53940 5.0 5.0 19.8
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)
2.0 2.07 96.7 0.464 -- 1.3 1.96 5580

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 2.0 39.85 -- 0.0 55735 53915 2694 96.6 -- 0.235 0.235 0.276 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 2.0 2.13 8393 462 8393 0.403 0.403 0.019 95.3
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 40.0
Anisotropic B[1][1] -5.35
Anisotropic B[1][2] 0.86
Anisotropic B[1][3] 6.8
Anisotropic B[2][2] -3.77
Anisotropic B[2][3] -1.63
Anisotropic B[3][3] 9.12
RMS Deviations
Key Refinement Restraint Deviation
c_bond_d 0.007
c_improper_angle_d 0.83
c_angle_deg 1.2
c_scbond_it 2.43
c_mcangle_it 2.31
c_scangle_it 3.59
c_dihedral_angle_d 21.3
c_mcbond_it 1.43
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.31
Luzzati Sigma A (Observed) 0.54
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.35
Luzzati Sigma A (R-Free Set) 0.56
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5050
Nucleic Acid Atoms 0
Heterogen Atoms 34
Solvent Atoms 484

Software

Software
Software Name Purpose
CNS refinement version: 1.1
CrystalClear data collection
d*TREK data reduction
d*TREK data scaling
PHASER phasing