X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.5
Temperature 298.0
Details The purified ParC55 protein was dialyzed against 20 mM Tris-HCl, pH 7.0, 200 mM NaCl, 10% glycerol, 1 mM beta-mercaptoethanol, 0.05% NaN3 then concentrated to 3-4 mg/ml. Hanging drops were formed by mixing equal volumes of protein and crystallization solutions (100 mM Tris-HCl, pH 5.5, 200 mM NaCl, 1 mM beta-mercaptoethanol, 0.05% NaN3 and 10% of 1:1 ethanol-isopropanol as precipitant). , VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 136.92 α = 90
b = 137.85 β = 90
c = 326.02 γ = 90
Symmetry
Space Group I 2 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MAR scanner 345 mm plate two cylindrical parabolic mirrors --
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE BM30A 0.91694 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
2.67 -- -- -- 0.093 -- 5.4 -- 85197 -- -- --

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 2.67 500.0 -- -- -- 85197 8219 97.2 -- -- 0.2235 0.2758 RANDOM
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 64.915
Anisotropic B[1][1] -7.871
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -6.113
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 13.983
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 2.224
c_mcangle_it 2.075
c_scbond_it 1.337
c_mcbond_it 1.163
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.39
Luzzati Sigma A (Observed) 0.73
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.46
Luzzati Sigma A (R-Free Set) 0.65
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 13620
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 24

Software

Computing
Computing Package Purpose
MAR 345DTB Data Collection
XDS Data Reduction (intensity integration)
XSCALE Data Reduction (data scaling)
CNS Structure Solution
CNS Structure Refinement
Software
Software Name Purpose
pdb_extract version: 2.000 data extraction
CNS refinement