X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 4.6
Temperature 20.0
Details Soaking in 30mM ATP, 40% PEG 2000, 10 mM ammonium sulphate, 0.1 M sodium citrate pH 4.6, 25mM magnesium acetate, 2 mM mercaptoethanol, 3 mM EDTA, 1.5 mM DTT, VAPOR DIFFUSION, HANGING DROP, SOAKING

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 75.51 α = 90
b = 75.51 β = 90
c = 136.02 γ = 120
Symmetry
Space Group P 65 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARRESEARCH Toroidal Mirror 2001-04-07
Diffraction Radiation
Monochromator Protocol
Silicon SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE BM30A 0.93 ESRF BM30A

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 24.72 99.8 -- 0.066 -- 6.5 20281 20281 0.0 -3.0 23.0
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)
1.85 1.95 98.8 -- 0.382 1.9 5.5 2839

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
OTHER 1.85 24.72 1967000.0 0.0 20223 20223 981 99.6 0.211 0.21 0.21 0.233 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 3084 149 3084 0.235 0.269 0.022 98.7
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 26.8
Anisotropic B[1][1] 2.95
Anisotropic B[1][2] -0.08
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 2.95
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -5.9
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 4.86
c_scbond_it 4.25
c_mcangle_it 1.68
c_mcbond_it 1.15
c_improper_angle_d 0.79
c_dihedral_angle_d 20.7
c_angle_deg 1.2
c_bond_d 0.005
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.21
Luzzati Sigma A (Observed) 0.12
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.24
Luzzati Sigma A (R-Free Set) 0.12
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1514
Nucleic Acid Atoms 0
Heterogen Atoms 75
Solvent Atoms 145

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
CCP4 (SCALA) Data Reduction (data scaling)
CNS 1.0 Structure Solution
CNS 1.0 Structure Refinement
Software
Software Name Purpose
CNS version: 1.0 refinement
CNS version: 1.0 model building
SCALA data reduction
DENZO data collection