X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.2
Temperature 280.0
Details 12% PEGM 5000; 170 mM NaCl; 50 mM HEPES (NaOH) pH 7.2; 5 mM MgCl2; 5 mM DTT; 0.5 mM EGTA; and 2% 2-methyl-1,3-propanediol, at 280 K, VAPOR DIFFUSION, SITTING DROP

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 135.42 α = 90
b = 155.42 β = 90
c = 143.19 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARRESEARCH -- 1999-01-01
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID13 1.000 ESRF ID13

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
-- -- -- -- -- -- -- -- n/a -- -- 52.3

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
-- 2.8 41.15 -- 0.0 -- 73283 5989 97.7 -- 0.232 0.232 0.29 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 2.8 2.98 -- 962 11122 0.328 0.379 0.012 97.8
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 52.7
Anisotropic B[1][1] -11.56
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -7.69
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 19.25
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 3.57
c_scbond_it 2.3
c_mcangle_it 2.68
c_mcbond_it 1.57
c_improper_angle_d 0.79
c_dihedral_angle_d 21.7
c_angle_deg 1.3
c_bond_d 0.008
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.37
Luzzati Sigma A (Observed) 0.42
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.48
Luzzati Sigma A (R-Free Set) 0.53
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 16222
Nucleic Acid Atoms 0
Heterogen Atoms 56
Solvent Atoms 14

Software

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