X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.7
Temperature 293.0
Details Drops were formed by mixing equal amounts of 20 mg/ml protein in 50 mM HEPES pH 7.7, 400 mM NaCl, 30% glycerol, 1 mM EDTA and 10 mM N,N-dimethylundecylamin-N-oxide (C11DAO) with a precipitant solution of 0.1 M acetate pH 4.6 5.0, 40 mM C11DAO, 20.8 mM N,N-dimethyldecylamine-N-oxide (DDAO), 2 mM dihydroorotate (DHO), 1.8 2.4 M ammonium sulfate, 1 mM compound. The hanging drops were incubated against 0.5 mL reservoir of 0.1 M acetate pH 4.8, 2.4 2.6 M ammonium sulfate and 30% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 90.29 α = 90
b = 90.29 β = 90
c = 122.69 γ = 120
Symmetry
Space Group P 32 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARRESEARCH -- 2003-11-24
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON MPG/DESY, HAMBURG BEAMLINE BW6 1.05 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
1.9 18 98.6 0.065 -- -- -- -- 41032 1.0 1.0 8.7
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)
1.9 2.05 99.0 0.24 -- 4.9 -- 39080

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 2.0 17.22 -- 0.0 -- 41032 1965 98.5 -- -- 0.181 0.2 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 2.0 2.13 6438 335 6103 0.197 0.22 0.012 99.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 21.7
Anisotropic B[1][1] 1.64
Anisotropic B[1][2] 1.78
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.64
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -3.29
RMS Deviations
Key Refinement Restraint Deviation
c_mcangle_it 1.64
c_mcbond_it 1.11
c_improper_angle_d 0.8
c_angle_deg 1.2
c_bond_d 0.005
c_scangle_it 3.14
c_dihedral_angle_d 21.2
c_scbond_it 2.08
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.19
Luzzati Sigma A (Observed) 0.09
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.22
Luzzati Sigma A (R-Free Set) 0.11
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2785
Nucleic Acid Atoms 0
Heterogen Atoms 101
Solvent Atoms 291

Software

Software
Software Name Purpose
CNS refinement
PDB_EXTRACT data extraction version: 1.701
DENZO data reduction
SCALEPACK data scaling
MOLREP phasing
CNX refinement version: 2002