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P. putida mandelate racemase co-crystallized with the intermediate analogue benzohydroxamate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2MNR PDB ENTRY 2MNR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 298 14% (w/v) PEG1500, 200mM glycine, 50mM NaI, 100mM Triethanolamine pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.82 56.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 148.309 α = 90 b = 148.309 β = 90 c = 169.552 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 225 mm CCD 2010-10-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.978 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.2 50 100 0.105 28 7.6 92408 92311 -3 27.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.24 100 0.253 8.3 7.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2MNR 2.201 50 87693 4618 99.82 0.16332 0.16174 0.1626 0.19325 0.1934 RANDOM 17.361
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] -0.61 -0.61 1.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.033 r_dihedral_angle_4_deg 20.115 r_dihedral_angle_3_deg 12.679 r_dihedral_angle_1_deg 5.583 r_angle_refined_deg 1.355 r_chiral_restr 0.087 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.033 r_dihedral_angle_4_deg 20.115 r_dihedral_angle_3_deg 12.679 r_dihedral_angle_1_deg 5.583 r_angle_refined_deg 1.355 r_chiral_restr 0.087 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_it r_mcbond_other r_mcangle_it r_scbond_it r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10746 Nucleic Acid Atoms Solvent Atoms 749 Heterogen Atoms 44
Software Software Software Name Purpose MD2 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling