X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 293.0
Details PEG 8000, Tris-HCl, NaCl, dithiothreitol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 57.86 α = 90
b = 69.58 β = 90
c = 89.26 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS II mirrors 2000-06-29
Diffraction Radiation
Monochromator Protocol
YALE MIRRORS SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RU200 1.5418 -- --

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
2.4 30 99.0 0.064 -- -- 3.2 14350 14350 0.0 0.0 17.5
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)
2.4 2.49 93.9 0.223 -- -- -- --

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
MOLECULAR REPLACEMENT 2.4 30.0 0.0 0.0 13915 13915 702 96.0 -- 0.21 0.21 0.268 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 2.4 2.55 -- 96 1894 0.238 0.336 0.034 83.7
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 25.9
Anisotropic B[1][1] -1.42
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.63
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.79
RMS Deviations
Key Refinement Restraint Deviation
c_improper_angle_d 0.72
c_angle_deg 1.3
c_mcbond_it 1.46
c_scbond_it 2.45
c_mcangle_it 2.37
c_bond_d 0.007
c_dihedral_angle_d 22.0
c_scangle_it 3.57
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.28
Luzzati Sigma A (Observed) 0.24
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.39
Luzzati Sigma A (R-Free Set) 0.39
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2205
Nucleic Acid Atoms 0
Heterogen Atoms 32
Solvent Atoms 141

Software

Software
Software Name Purpose
AMoRE phasing
CNS refinement version: 0.5
DENZO data reduction
SCALEPACK data scaling