X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.5
Temperature 291.0
Details reservoir: 100 mM sodium cacodylate, 15% glycerol, 10.5% PEG8000, 500 mM (NH4)2(SO4). drop: 0.002 ml protein (16mg/ml) in 20mM Tris/HCl pH 7.5, 1mM EDTA, 1mM NaN3, 0.002 ml reservoir, 0.0005 ml 1.0 M guanidinium chloride, 0.0005 ml C12E8 (octaethylene glycol monododecyl ether), pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 208.15 α = 90
b = 167.7 β = 90
c = 108.19 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MARRESEARCH MIRROR 1999-08-15
Diffraction Radiation
Monochromator Protocol
DOUBLE CRYSTAL SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON MPG/DESY, HAMBURG BEAMLINE BW6 -- MPG/DESY, HAMBURG BW6

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
3 35 96.9 0.079 7.9 -- 3.0 265668 74040 -- -- 55.1
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)
3.0 3.05 96.0 0.526 52.6 -- 2.7 --

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 3.0 25.0 -- 0.0 -- 73947 3765 96.8 -- 0.294 0.294 0.342 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 3.0 3.19 -- 595 11466 0.399 0.427 0.018 96.1
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 55.1
Anisotropic B[1][1] -5.64
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 23.64
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -18.0
RMS Deviations
Key Refinement Restraint Deviation
c_improper_angle_d 0.79
c_angle_deg 1.3
c_dihedral_angle_d 21.4
c_bond_d 0.009
c_scbond_it 10.51
c_mcbond_it 4.09
c_scangle_it 12.49
c_mcangle_it 5.69
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.46
Luzzati Sigma A (Observed) 0.54
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.55
Luzzati Sigma A (R-Free Set) 0.61
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 19230
Nucleic Acid Atoms 0
Heterogen Atoms 136
Solvent Atoms 0

Software

Software
Software Name Purpose
AMoRE phasing
CNS refinement version: 0.9
DENZO data reduction
SCALEPACK data scaling