X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 273.0
Details Na phosphate, K phosphate, Na acetate, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 273K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 100.2 α = 90
b = 100.2 β = 90
c = 364.66 γ = 90
Symmetry
Space Group P 43 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS V mirrors 2001-02-26
Diffraction Radiation
Monochromator Protocol
diamond SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL45PX 1.02 SPring-8 BL45PX

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
2.3 50 98.4 0.107 0.107 -- 6.9 567949 567949 -- -- 15.0
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)
2.3 2.34 96.7 0.382 0.382 3.78 4.6 3973

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 2.3 50.0 0.0 0.0 -- 82093 8228 98.3 -- 0.229 0.229 0.271 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 2.3 2.44 -- 1259 11665 0.329 0.358 0.01 94.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 35.7
Anisotropic B[1][1] 4.82
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 4.82
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -9.65
RMS Deviations
Key Refinement Restraint Deviation
c_improper_angle_d 0.87
c_mcbond_it 1.23
c_mcangle_it 2.01
c_bond_d 0.007
c_scbond_it 2.01
c_angle_deg 1.3
c_dihedral_angle_d 22.6
c_scangle_it 3.04
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.32
Luzzati Sigma A (Observed) 0.42
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.37
Luzzati Sigma A (R-Free Set) 0.47
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 9304
Nucleic Acid Atoms 0
Heterogen Atoms 15
Solvent Atoms 184

Software

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