X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 298.0
Details PEG1500, DTT, HEPES; NA OR K PHOSPHATE, DTT, HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 59.63 α = 90
b = 111.64 β = 95.89
c = 59.9 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 298
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS II -- 1997-03-22
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RU200 -- -- --

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
2.5 40.65 79.9 0.063 -- -- 2.632 27035 21222 0.0 0.0 18.4
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)
2.5 2.54 66.8 0.203 -- -- 1.35 --

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
-- 2.5 40.65 0.0 2.0 27035 20603 1617 76.2 0.172 0.166 0.155 0.214 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 2.5 2.66 -- 233 2589 0.198 0.294 0.019 63.3
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 26.2
Anisotropic B[1][1] -0.06
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.1
Anisotropic B[2][2] 0.58
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.52
RMS Deviations
Key Refinement Restraint Deviation
c_bond_d 0.007
c_mcbond_it 2.1
c_improper_angle_d 0.89
c_mcangle_it 3.22
c_scbond_it 3.39
c_scangle_it 4.67
c_dihedral_angle_d 24.1
c_angle_deg 1.3
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.21
Luzzati Sigma A (Observed) 0.22
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.32
Luzzati Sigma A (R-Free Set) 0.37
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5820
Nucleic Acid Atoms 0
Heterogen Atoms 30
Solvent Atoms 196

Software

Software
Software Name Purpose
AMoRE phasing
CNS refinement version: 0.9
DENZO data reduction
SCALEPACK data scaling