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_scangle_it 3.04
c_scbond_it 2.01
c_mcangle_it 2.01
c_mcbond_it 1.23
c_improper_angle_d 0.87
c_bond_d 0.007
c_angle_deg 1.3
c_dihedral_angle_d 22.6
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

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
AMORE Structure Solution
CNS Structure Refinement
Software
Software Name Purpose
CNS refinement
AMoRE model building