X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 296.0
Details 2M AMMONIUM SULFATE, 100MM HEPES PH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 113.85 α = 90
b = 113.85 β = 90
c = 233.87 γ = 120
Symmetry
Space Group P 61 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MARRESEARCH -- 1998-10-01
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 5ID-B -- APS 5ID-B

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
2.15 29 91.7 0.048 -- -- 5.7 259275 45125 0.0 0.0 39.8
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)
2.15 2.21 85.8 0.261 -- -- 3.8 --

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
-- 2.15 14.97 -- 2.0 44947 43571 2166 88.3 0.234 0.234 0.229 0.282 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 2.15 2.23 -- 178 3732 0.288 0.382 0.029 81.2
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 41.6
Anisotropic B[1][1] 0.93
Anisotropic B[1][2] 4.37
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.93
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.86
RMS Deviations
Key Refinement Restraint Deviation
c_improper_angle_d 0.88
c_scbond_it 1.16
c_scangle_it 2.0
c_angle_deg 1.4
c_bond_d 0.008
c_mcbond_it 1.09
c_dihedral_angle_d 23.7
c_mcangle_it 1.89
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.29
Luzzati Sigma A (Observed) 0.24
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.38
Luzzati Sigma A (R-Free Set) 0.33
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3939
Nucleic Acid Atoms 0
Heterogen Atoms 1
Solvent Atoms 380

Software

Software
Software Name Purpose
AMoRE phasing
REFMAC refinement
X-PLOR refinement
CNS refinement version: 0.9
DENZO data reduction
CCP4 data scaling version: (SCALA)