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Crystal structure of probable proline racemase from agrobacterium radiobacter K84, TARGET EFI-506561, with bound carbonate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4LB0 PDB ENTRY 4LB0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 15 MM BIS-TRIS, 500 MM NACL, 10% GLYCEROL, 5 MM DTT, TEV PROTEASE (1:100 RATIO); RESERVOIR: 0.4 M POTASSIUM PHOSPHATE MONOBASIC, 16% PEG8000, 20% GLYCEROL, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.49 50.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.43 α = 90 b = 129.47 β = 90 c = 178.703 γ = 90
Symmetry Space Group C 2 2 21
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 RAYONIX MX225HE MIRRORS 2014-02-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID APS 31-ID
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) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.8 50 99.9 0.085 0.085 20.9 7.3 72154 -5 25.997
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) Redundancy Number Unique Reflections (All) 1 1.8 1.83 100 0.91 0.91 2.3 7.4
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 4LB0 1.8 30 69949 2156 99.64 0.14744 0.14656 0.1605 0.1757 0.185 RANDOM 35.503
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] -0.47 1.83 -1.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.797 r_dihedral_angle_4_deg 18.207 r_dihedral_angle_3_deg 13.115 r_long_range_B_refined 11.51 r_long_range_B_other 11.509 r_scbond_it 11.235 r_scbond_other 11.233 r_scangle_other 10.943 r_dihedral_angle_1_deg 5.968 r_mcbond_it 4.689
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.797 r_dihedral_angle_4_deg 18.207 r_dihedral_angle_3_deg 13.115 r_long_range_B_refined 11.51 r_long_range_B_other 11.509 r_scbond_it 11.235 r_scbond_other 11.233 r_scangle_other 10.943 r_dihedral_angle_1_deg 5.968 r_mcbond_it 4.689 r_mcbond_other 4.689 r_mcangle_it 4.678 r_mcangle_other 4.677 r_angle_refined_deg 1.349 r_angle_other_deg 0.74 r_chiral_restr 0.081 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 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 5102 Nucleic Acid Atoms Solvent Atoms 679 Heterogen Atoms 14
Software Software Software Name Purpose PHASER phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling