4M6U

P. putida mandelate racemase co-crystallized with tartronic acid


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2MNRPDB ENTRY 2MNR

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.529814% (w/v) PEG 1500, 100 mM glycine, 100 mM Triethanolamine (pH 8.5), VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
359

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 149.35α = 90
b = 149.35β = 90
c = 177.752γ = 90
Symmetry
Space GroupI 4 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2013-06-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G0.979APS21-ID-G

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
11.85098.80.07329.510.19129190212-313.6
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)
11.81.8399.80.37658.74535

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 2MNR1.832.3886721457098.740.147840.146620.17073RANDOM20.043
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]
-0.87-0.871.73
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.063
r_dihedral_angle_4_deg17.706
r_dihedral_angle_3_deg13.002
r_dihedral_angle_1_deg6.24
r_long_range_B_refined4.925
r_long_range_B_other4.558
r_scangle_other3.18
r_mcangle_it2.383
r_mcangle_other2.382
r_scbond_it2.141
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.063
r_dihedral_angle_4_deg17.706
r_dihedral_angle_3_deg13.002
r_dihedral_angle_1_deg6.24
r_long_range_B_refined4.925
r_long_range_B_other4.558
r_scangle_other3.18
r_mcangle_it2.383
r_mcangle_other2.382
r_scbond_it2.141
r_scbond_other2.138
r_angle_refined_deg1.754
r_mcbond_it1.616
r_mcbond_other1.616
r_angle_other_deg0.92
r_chiral_restr0.122
r_bond_refined_d0.017
r_gen_planes_refined0.009
r_gen_planes_other0.003
r_bond_other_d0.001
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5377
Nucleic Acid Atoms
Solvent Atoms637
Heterogen Atoms18

Software

Software
Software NamePurpose
MD2data collection
PHASERphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling