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P. putida mandelate racemase co-crystallized with tartronic acid
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 8.5 298 14% (w/v) PEG 1500, 100 mM glycine, 100 mM Triethanolamine (pH 8.5), VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3 59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 149.35 α = 90 b = 149.35 β = 90 c = 177.752 γ = 90
Symmetry Space Group I 4 2 2
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 300 mm CCD 2013-06-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.979 APS 21-ID-G
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 1.8 50 98.8 0.073 29.5 10.1 91291 90212 -3 13.6
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 1.8 1.83 99.8 0.376 5 8.7 4535
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 1.8 32.38 86721 4570 98.74 0.14784 0.14662 0.1605 0.17073 0.1829 RANDOM 20.043
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 -0.87 1.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.063 r_dihedral_angle_4_deg 17.706 r_dihedral_angle_3_deg 13.002 r_dihedral_angle_1_deg 6.24 r_long_range_B_refined 4.925 r_long_range_B_other 4.558 r_scangle_other 3.18 r_mcangle_it 2.383 r_mcangle_other 2.382 r_scbond_it 2.141
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.063 r_dihedral_angle_4_deg 17.706 r_dihedral_angle_3_deg 13.002 r_dihedral_angle_1_deg 6.24 r_long_range_B_refined 4.925 r_long_range_B_other 4.558 r_scangle_other 3.18 r_mcangle_it 2.383 r_mcangle_other 2.382 r_scbond_it 2.141 r_scbond_other 2.138 r_angle_refined_deg 1.754 r_mcbond_it 1.616 r_mcbond_other 1.616 r_angle_other_deg 0.92 r_chiral_restr 0.122 r_bond_refined_d 0.017 r_gen_planes_refined 0.009 r_gen_planes_other 0.003 r_bond_other_d 0.001 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 Atoms Number Protein Atoms 5377 Nucleic Acid Atoms Solvent Atoms 637 Heterogen Atoms 18
Software Software Software Name Purpose MD2 data collection PHASER phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling