X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8
Temperature 281.0
Details PEG 8000, sodium chloride, hepes, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 281.0K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 59.91 α = 90
b = 99.07 β = 97.34
c = 58.63 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 double crystal monochromator 2000-03-03
Diffraction Radiation
Monochromator Protocol
double crystal monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL9-2 1.0 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
1.4 59.76 88.2 0.031 0.031 -- 2.52 293233 116635 2.0 2.0 18.0
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)
1.4 1.42 58.0 0.117 0.117 5.8 1.3 3860

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 1.45 21.82 0.0 0.0 116635 108126 10852 90.2 0.205 0.205 0.205 0.228 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 1.45 1.52 108126 1105 10158 0.27 0.298 0.009 75.7
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 21.7
Anisotropic B[1][1] -2.6
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.85
Anisotropic B[2][2] 0.63
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.97
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 4.68
c_scbond_it 3.01
c_mcangle_it 2.82
c_mcbond_it 1.82
c_improper_angle_d 1.07
c_dihedral_angle_d 23.9
c_angle_deg 1.5
c_bond_d 0.008
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.18
Luzzati Sigma A (Observed) 0.11
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.2
Luzzati Sigma A (R-Free Set) 0.14
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4582
Nucleic Acid Atoms 0
Heterogen Atoms 4
Solvent Atoms 540

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