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_mcbond_it 1.163
c_scbond_it 1.337
c_scangle_it 2.224
c_mcangle_it 2.075
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

Software
Software Name Purpose
CNS refinement
PDB_EXTRACT data extraction version: 2.000
MAR345 data collection version: 345DTB
XDS data reduction
XSCALE data scaling
CNS phasing