X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 277.0
Details 100 mM sodium cacodylate pH 6.5, 200 mM calcium acetate, 16-18% PEG, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 92.11 α = 90
b = 92.11 β = 90
c = 211.01 γ = 120
Symmetry
Space Group P 65 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD SBC-1 -- 2000-03-07
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-ID -- 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
2.6 30 96.6 0.073 -- -- 4.74 18214 17653 2.0 1.0 35.4
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)
2.54 2.69 99.8 0.352 -- -- 3.15 1757

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
-- 2.6 29.85 1.0 2.0 17058 14841 1505 87.0 -- 0.221 0.221 0.27 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 2.6 2.76 -- 175 1752 0.264 0.361 0.027 69.9
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 40.6
Anisotropic B[1][1] 4.05
Anisotropic B[1][2] 6.93
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 4.05
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -8.1
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 2.3
c_scbond_it 1.46
c_mcangle_it 1.98
c_mcbond_it 1.15
c_improper_angle_d 0.9
c_dihedral_angle_d 20.7
c_angle_deg 1.3
c_bond_d 0.006
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.32
Luzzati Sigma A (Observed) 0.32
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.42
Luzzati Sigma A (R-Free Set) 0.46
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2439
Nucleic Acid Atoms 598
Heterogen Atoms 1
Solvent Atoms 132

Software

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