X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4.5
Temperature 293.0
Details 8.6mM ATP, 30mM Magnesium chloride, 40% 1,2-propanediol, 100mM sodium acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 38.91 α = 78.91
b = 53.77 β = 72.12
c = 63.43 γ = 69.66
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RIGAKU JUPITER 210 -- 2006-10-02
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL26B2 1.0 SPring-8 BL26B2

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
1.7 36.82 95.1 -- -- -- -- 50234 47774 -- -- 13.0
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)
1.7 1.76 90.9 -- -- -- -- --

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 1.7 36.82 -- 0.0 50234 47774 4813 95.1 -- 0.184 0.184 0.218 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 1.7 1.81 -- 763 6975 0.205 0.251 0.009 92.7
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 15.4
Anisotropic B[1][1] -1.44
Anisotropic B[1][2] -2.98
Anisotropic B[1][3] 0.63
Anisotropic B[2][2] 4.11
Anisotropic B[2][3] 1.52
Anisotropic B[3][3] -2.66
RMS Deviations
Key Refinement Restraint Deviation
c_bond_d 0.005
c_mcangle_it 1.56
c_improper_angle_d 0.79
c_dihedral_angle_d 22.2
c_scbond_it 1.87
c_angle_deg 1.3
c_mcbond_it 1.07
c_scangle_it 2.7
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.17
Luzzati Sigma A (Observed) 0.08
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.21
Luzzati Sigma A (R-Free Set) 0.14
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3808
Nucleic Acid Atoms 0
Heterogen Atoms 128
Solvent Atoms 460

Software

Software
Software Name Purpose
BSS data collection
AMoRE phasing
CNS refinement version: 1.1
HKL-2000 data reduction
HKL-2000 data scaling