2WBP

Crystal structure of VioC in complex with Fe(II), (2S,3S)- hydroxyarginine, and succinate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2OG5PDB ENTRY 2OG5

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18.51.0 M NA-SUCCINATE, 0.1 M TRIS/HCL PH 8.0, 3 MM (2S\,3S)-HYDROXYARGININE
Crystal Properties
Matthews coefficientSolvent content
2.0339.53

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.77α = 90
b = 66.93β = 109.16
c = 62.9γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMIRRORS2008-07-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-2ESRFID23-2

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
11.162091.30.0610.6399570-3
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)
11.161.1951.10.252.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2OG51.1619.9697778179191.30.132930.132240.17099RANDOM13.984
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]
0.09-0.61-0.32-0.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.726
r_sphericity_free21.528
r_dihedral_angle_4_deg18.264
r_dihedral_angle_3_deg13.705
r_scangle_it9.548
r_sphericity_bonded8.402
r_scbond_it7.79
r_dihedral_angle_1_deg7.198
r_mcangle_it6.612
r_mcbond_it5.537
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.726
r_sphericity_free21.528
r_dihedral_angle_4_deg18.264
r_dihedral_angle_3_deg13.705
r_scangle_it9.548
r_sphericity_bonded8.402
r_scbond_it7.79
r_dihedral_angle_1_deg7.198
r_mcangle_it6.612
r_mcbond_it5.537
r_rigid_bond_restr4.69
r_mcbond_other2.996
r_angle_refined_deg1.355
r_angle_other_deg0.809
r_symmetry_vdw_other0.398
r_symmetry_vdw_refined0.262
r_nbd_other0.24
r_xyhbond_nbd_refined0.228
r_nbd_refined0.224
r_symmetry_hbond_refined0.223
r_nbtor_refined0.179
r_chiral_restr0.089
r_nbtor_other0.087
r_gen_planes_refined0.011
r_bond_refined_d0.01
r_gen_planes_other0.004
r_bond_other_d0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2595
Nucleic Acid Atoms
Solvent Atoms387
Heterogen Atoms40

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing