3OKP

Crystal structure of Corynebacterium glutamicum PimB' bound to GDP-Man (orthorhombic crystal form)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3OKAPDB entry 3oka

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION6.12910.1 M DL-malic acid pH 6.1, 13% PEG 3350 , VAPOR DIFFUSION, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.5151.08

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.746α = 90
b = 87.002β = 90
c = 106.895γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2010-02-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.9763DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
1237.291000.0960.09618.37.2289972899715.9
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
22.1199.80.380.385.77.24147

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 3oka237.292751927519147699.930.204080.202560.2321RANDOM14.231
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]
-0.210.050.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.301
r_dihedral_angle_3_deg12.804
r_dihedral_angle_4_deg11.101
r_dihedral_angle_1_deg4.856
r_scangle_it1.076
r_angle_refined_deg1.022
r_scbond_it0.65
r_mcangle_it0.432
r_nbtor_refined0.292
r_mcbond_it0.259
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.301
r_dihedral_angle_3_deg12.804
r_dihedral_angle_4_deg11.101
r_dihedral_angle_1_deg4.856
r_scangle_it1.076
r_angle_refined_deg1.022
r_scbond_it0.65
r_mcangle_it0.432
r_nbtor_refined0.292
r_mcbond_it0.259
r_nbd_refined0.17
r_symmetry_vdw_refined0.166
r_xyhbond_nbd_refined0.091
r_symmetry_hbond_refined0.066
r_chiral_restr0.064
r_bond_refined_d0.007
r_gen_planes_refined0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2827
Nucleic Acid Atoms
Solvent Atoms175
Heterogen Atoms28

Software

Software
Software NamePurpose
ADSCdata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling