2WBQ

Crystal structure of VioC in complex with (2S,3S)-hydroxyarginine


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.50.6 M TRI-SODIUM CITRATE 0.1 M HEPES PH 7.5 3 MM (2S,3S)-HYDROXYARGININE
Crystal Properties
Matthews coefficientSolvent content
2.0339.38

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.91α = 90
b = 66.83β = 109.17
c = 62.73γ = 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
11.12096.80.0414.13.6123576-3
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)
11.11.1384.90.571.5

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 2OG51.119.75121303224996.80.1440.1430.178RANDOM14.18
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]
-0.31-0.98-0.390.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.153
r_dihedral_angle_4_deg17.46
r_scangle_it13.345
r_dihedral_angle_3_deg12.884
r_scbond_it11.799
r_mcangle_it7.913
r_mcbond_it7.25
r_dihedral_angle_1_deg6.786
r_angle_refined_deg1.449
r_angle_other_deg1.282
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.153
r_dihedral_angle_4_deg17.46
r_scangle_it13.345
r_dihedral_angle_3_deg12.884
r_scbond_it11.799
r_mcangle_it7.913
r_mcbond_it7.25
r_dihedral_angle_1_deg6.786
r_angle_refined_deg1.449
r_angle_other_deg1.282
r_symmetry_vdw_other0.417
r_symmetry_hbond_refined0.28
r_symmetry_vdw_refined0.255
r_nbd_other0.253
r_xyhbond_nbd_refined0.236
r_nbd_refined0.229
r_nbtor_refined0.183
r_chiral_restr0.087
r_nbtor_other0.083
r_bond_refined_d0.011
r_gen_planes_refined0.009
r_gen_planes_other0.005
r_bond_other_d0.002
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_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2594
Nucleic Acid Atoms
Solvent Atoms461
Heterogen Atoms17

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing