X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 298.0
Details 1.4M Na(AC), Sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 76.78 α = 90
b = 76.78 β = 90
c = 107.39 γ = 120
Symmetry
Space Group P 32 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD SBC-2 mirrors 2002-07-02
Diffraction Radiation
Monochromator Protocol
Si 111 channel MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-ID 0.9795,0.9797,0.94656 APS 19-ID

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
2.5 50 99.0 0.079 -- -- 7.8 13046 12916 2.0 4.0 33.9
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 98.4 0.492 -- 2.24 6.0 1276

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
MAD 2.51 36.15 0.0 0.0 24343 21398 1021 87.9 -- 0.234 0.234 0.294 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 2.66 -- 133 2628 0.401 0.443 0.038 67.7
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 63.5
Anisotropic B[1][1] 11.76
Anisotropic B[1][2] 9.91
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 11.76
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -23.52
RMS Deviations
Key Refinement Restraint Deviation
c_bond_d 0.01
c_dihedral_angle_d 21.3
c_improper_angle_d 0.79
c_angle_deg 1.2
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.41
Luzzati Sigma A (Observed) 0.61
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.48
Luzzati Sigma A (R-Free Set) 0.55
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2133
Nucleic Acid Atoms 0
Heterogen Atoms 8
Solvent Atoms 29

Software

Computing
Computing Package Purpose
DTCOLLECT Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
CNS Structure Solution
CNS Structure Refinement
Software
Software Name Purpose
CNS version: 0.9 refinement