2G9D

Crystal Structure of Succinylglutamate desuccinylase from Vibrio cholerae, Northeast Structural Genomics Target VcR20


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Microbatch
pH 7
Temperature 291.0
Details 100 mM MOPS, 2880 mM Potassium Acetate, 5 mM DDT, pH 7.0, Microbatch, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 82.93 α = 90
b = 82.93 β = 90
c = 116.67 γ = 120
Symmetry
Space Group P 65

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 mirrors 2006-01-18
Diffraction Radiation
Monochromator Protocol
Si 111 CHANNEL MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X4A 0.97929, 0.97944, 0.96794 NSLS X4A

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 23.94 99.6 0.069 0.065 -- 6.2 17694 17624 0.0 0.0 --
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)
3.0 3.11 100.0 0.332 0.355 6.1 6.3 --

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
MAD 3.0 23.94 -- 2.0 17624 17351 1671 96.6 -- 0.241 0.241 0.272 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 -- 267 2484 0.333 0.363 0.022 90.1
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model OVERALL
Mean Isotropic B 63.1
Anisotropic B[1][1] 1.19
Anisotropic B[1][2] 14.35
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.19
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.38
RMS Deviations
Key Refinement Restraint Deviation
c_improper_angle_d 0.91
c_angle_deg 1.3
c_dihedral_angle_d 23.7
c_bond_d 0.008
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.4
Luzzati Sigma A (Observed) 0.48
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.46
Luzzati Sigma A (R-Free Set) 0.51
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2735
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 17

Software

Software
Software Name Purpose
CNS refinement version: 1.1
DENZO data reduction
SCALEPACK data scaling
SHELX phasing
SOLVE phasing
RESOLVE phasing