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Crystal structure of a 4-hydroxyproline epimerase from Burkholderia Multivorans atcc 17616, target EFI-506586, open form, with bound pyrrole-2-carboxylate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4K7X PDB ENTRY 4K7X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8 PROTEIN (10 MM TRIS, 150 MM NACL, 5% GLYCEROL, 5 MM DTT); RESERVOIR (0.1 M IMIDAZOLE:HCL, PH 8.0, 1 M AMMONIUM PHOSPHATE DIBASIC (MCSG3 A4), CRYOPROTECTION: (RESERVOIR), VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K
Crystal Properties Matthews coefficient Solvent content 3.17 61.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.749 α = 90 b = 95.053 β = 90 c = 126.275 γ = 90
Symmetry Space Group P 21 21 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 ADSC QUANTUM 315 2014-03-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A NSLS X29A
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 2.1 50 99.9 0.1 0.1 19 7.2 58519 -5 39.412
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.14 98.7 1.6 6.4
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 4K7X 2.1 50 56649 1801 99.66 0.17019 0.16874 0.1765 0.21488 0.2179 RANDOM 51.823
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] 2.88 -2.28 -0.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.077 r_long_range_B_refined 15.011 r_long_range_B_other 15.01 r_scangle_other 13.829 r_scbond_it 13.601 r_scbond_other 13.598 r_dihedral_angle_3_deg 12.827 r_dihedral_angle_4_deg 12.822 r_mcbond_other 8.665 r_mcbond_it 8.664
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.077 r_long_range_B_refined 15.011 r_long_range_B_other 15.01 r_scangle_other 13.829 r_scbond_it 13.601 r_scbond_other 13.598 r_dihedral_angle_3_deg 12.827 r_dihedral_angle_4_deg 12.822 r_mcbond_other 8.665 r_mcbond_it 8.664 r_mcangle_it 8.277 r_mcangle_other 8.276 r_dihedral_angle_1_deg 5.475 r_angle_refined_deg 1.161 r_angle_other_deg 0.689 r_chiral_restr 0.07 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 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 4621 Nucleic Acid Atoms Solvent Atoms 450 Heterogen Atoms 22
Software Software Software Name Purpose PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling