X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.5
Temperature 295.0
Details NaCl, Na-Cit., PEG400, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 49.86 α = 90
b = 85.19 β = 90
c = 87.58 γ = 90
Symmetry
Space Group I 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 93
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- --
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL9-2 -- SSRL BL9-2

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
1.95 30 98.7 0.084 -- -- 3.9 13874 n/a -- -- 21.4
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)
1.95 2.02 97.7 0.775 -- 2.4 3.4 1361

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 1.95 27.62 0.0 0.0 -- 13099 1340 93.7 -- 0.215 0.215 0.227 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 1.95 2.07 -- 188 1762 0.293 0.326 0.024 85.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 31.2
Anisotropic B[1][1] 0.08
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -6.16
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 6.07
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 2.65
c_scbond_it 1.84
c_mcangle_it 2.13
c_mcbond_it 1.47
c_improper_angle_d 0.74
c_dihedral_angle_d 24.5
c_angle_deg 1.4
c_bond_d 0.007
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.25
Luzzati Sigma A (Observed) 0.26
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.26
Luzzati Sigma A (R-Free Set) 0.31
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 986
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 77

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
AMORE Structure Solution
CNS 1.0 Structure Refinement
Software
Software Name Purpose
CNS version: 1.0 refinement
AMORE model building
SCALEPACK data reduction
DENZO data collection