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Crystal structure of a 4-hydroxyproline epimerase from burkholderia multivorans, target efi-506479, with bound phosphate, closed domains
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4J9W
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.2 298 Protein (10 mM Tris, 150 mM NaCl, 5% glycerol, 5 mM BME, 20 mM pyrrole 2-carboxylate); Reservoir (0.1 M Phosphate-citrate, 1.6 M NaH2PO4/0.4 M K2HPO4 (MCSG2 E10)); Cryoprotection (Reservoir+20% glycerol), pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 4.04 69.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.885 α = 90 b = 114.885 β = 90 c = 173.699 γ = 90
Symmetry Space Group I 41 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 RAYONIX 225 HE MIRRORS 2012-04-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.9793 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 1.75 95.823 100 0.13 0.13 14.1 14.3 58608 58608
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 1.75 1.84 100 0.699 0.699 1.1 13.5 8443
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 4J9W 1.75 28.779 58574 58574 2964 99.98 0.138 0.138 0.137 0.1386 0.1564 0.1574 RANDOM 18.4258
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 11.742 f_angle_d 1.268 f_chiral_restr 0.079 f_bond_d 0.009 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2346 Nucleic Acid Atoms Solvent Atoms 463 Heterogen Atoms 33
Software Software Software Name Purpose SCALA data scaling PHENIX refinement PDB_EXTRACT data extraction MOSFLM data reduction AMoRE phasing