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_angle_deg 2.0
c_bond_d 0.01
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

Software
Software Name Purpose
AMoRE phasing
CNS refinement
DENZO data reduction
SCALEPACK data scaling