X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 290.0
Details sodium citrate, magnesium chloride, Na-HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290.0K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 251.45 α = 90
b = 251.45 β = 90
c = 88.7 γ = 120
Symmetry
Space Group P 63

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 123
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MARRESEARCH -- --
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON LURE BEAMLINE DW32 -- LURE DW32

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
3 15 91.9 0.088 -- -- 3.9 58634 58634 -- -- 51.1
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)
3.0 3.11 98.3 0.239 -- -- 3.9 6249

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
-- 3.0 15.0 -- 0.0 58634 58634 2969 91.8 -- 0.248 0.248 0.293 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 3.0 3.19 -- 509 9874 0.344 0.39 0.017 98.3
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 40.2
Anisotropic B[1][1] 5.61
Anisotropic B[1][2] 16.85
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 5.61
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -11.21
RMS Deviations
Key Refinement Restraint Deviation
c_improper_angle_d 2.18
c_bond_d 0.01
c_angle_deg 2.0
c_dihedral_angle_d 27.9
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.4
Luzzati Sigma A (Observed) 0.5
Luzzati Resolution Cutoff (Low) 6.0
Luzzati ESD (R-Free Set) 0.49
Luzzati Sigma A (R-Free Set) 0.62
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 9336
Nucleic Acid Atoms 3140
Heterogen Atoms 0
Solvent Atoms 96

Software

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