2WOK

Clavulanic acid biosynthesis oligopeptide binding protein 2 complexed with bradykinin


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2WOLPDB ENTRY 2WOL

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18pH 8
Crystal Properties
Matthews coefficientSolvent content
2.346

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.511α = 90
b = 83.327β = 95.54
c = 62.38γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDM2007-12-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-3ESRFID14-3

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
11.762.199.70.1183.75988519.2
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)
11.71.7499.80.442.63.7

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 2WOL1.762.1456831302299.750.186550.184620.22268RANDOM18.119
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]
-1.060.181.54-0.45
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.159
r_dihedral_angle_4_deg19.913
r_dihedral_angle_3_deg12.695
r_dihedral_angle_1_deg5.674
r_scangle_it3.803
r_scbond_it2.354
r_angle_refined_deg1.464
r_mcangle_it1.395
r_mcbond_it0.887
r_nbtor_refined0.308
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.159
r_dihedral_angle_4_deg19.913
r_dihedral_angle_3_deg12.695
r_dihedral_angle_1_deg5.674
r_scangle_it3.803
r_scbond_it2.354
r_angle_refined_deg1.464
r_mcangle_it1.395
r_mcbond_it0.887
r_nbtor_refined0.308
r_nbd_refined0.202
r_xyhbond_nbd_refined0.129
r_symmetry_vdw_refined0.126
r_symmetry_hbond_refined0.099
r_chiral_restr0.097
r_bond_refined_d0.014
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_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 Atoms4359
Nucleic Acid Atoms
Solvent Atoms380
Heterogen Atoms12

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing