X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6
Temperature 298.0
Details sodium citrate, lithium chloride, manganese chloride, alpha,beta-methylene-ADP, PEG monomethylether 5000, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 89.4 α = 110.79
b = 89.96 β = 106.43
c = 96.26 γ = 107.76
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MARRESEARCH -- 1999-10-20
Diffraction Radiation
Monochromator Protocol
BENT SINGLE-CRYSTAL GERMANIUM TRIANGULAR MONOCHROMATOR SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7B 0.8445 EMBL/DESY, Hamburg BW7B

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
1.85 50 97.1 0.038 -- -- 1.8 203784 203784 0.0 0.0 21.9
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)
1.85 1.92 93.2 0.39 -- -- -- --

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 1.85 28.59 0.0 0.0 198903 198903 1981 97.1 -- 0.207 0.207 0.234 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 1.85 1.97 -- 295 31863 0.301 0.331 0.019 94.2
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 34.1
Anisotropic B[1][1] -2.81
Anisotropic B[1][2] -0.48
Anisotropic B[1][3] 3.2
Anisotropic B[2][2] -3.04
Anisotropic B[2][3] 4.7
Anisotropic B[3][3] 5.84
RMS Deviations
Key Refinement Restraint Deviation
c_improper_angle_d 0.98
c_mcangle_it 1.93
c_scangle_it 2.77
c_mcbond_it 1.31
c_scbond_it 1.95
c_bond_d 0.011
c_angle_deg 1.6
c_dihedral_angle_d 23.8
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.24
Luzzati Sigma A (Observed) 0.2
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.28
Luzzati Sigma A (R-Free Set) 0.24
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 16400
Nucleic Acid Atoms 0
Heterogen Atoms 116
Solvent Atoms 1219

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
AMoRE phasing
CNS refinement version: 1.0