3EER

High resolution structure of putative organic hydroperoxide resistance protein from Vibrio cholerae O1 biovar eltor str. N16961


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
182910.2 M ZnAcetate, 0.1 M Imidazole, 20% Peg 3000, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.4650.02

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.649α = 90
b = 71.127β = 90
c = 71.629γ = 90
Symmetry
Space GroupI 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayCCDSBC-3MIRRORS2008-08-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-BMAPS19-BM

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.454099.10.10619.76.427234
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.451.4890.90.4642.342.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSADTHROUGHOUT1.4540227216258581358990.1410.1390.164RANDOM5.82
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
0.47-0.08-0.4
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.118
r_dihedral_angle_4_deg21.242
r_dihedral_angle_3_deg10.36
r_dihedral_angle_1_deg5.635
r_scangle_it3.316
r_scbond_it2.156
r_angle_refined_deg1.508
r_mcangle_it1.377
r_angle_other_deg0.986
r_mcbond_it0.843
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.118
r_dihedral_angle_4_deg21.242
r_dihedral_angle_3_deg10.36
r_dihedral_angle_1_deg5.635
r_scangle_it3.316
r_scbond_it2.156
r_angle_refined_deg1.508
r_mcangle_it1.377
r_angle_other_deg0.986
r_mcbond_it0.843
r_mcbond_other0.255
r_chiral_restr0.097
r_bond_refined_d0.015
r_gen_planes_refined0.007
r_bond_other_d0.003
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1009
Nucleic Acid Atoms
Solvent Atoms182
Heterogen Atoms39

Software

Software
Software NamePurpose
SBC-Collectdata collection
MOLREPphasing
CCP4model building
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
DMphasing
ARP/wARPmodel building
CCP4phasing
Cootmodel building