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Crystal structure of human trans-3-Hydroxy-L-proline dehydratase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6R77
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.5 293.15 0.1 M MES pH=6.5 12% (w/v) PEG 20000
Crystal Properties Matthews coefficient Solvent content 3.36 63.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.054 α = 90 b = 122.923 β = 90 c = 73.159 γ = 90
Symmetry Space Group P 21 21 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 PIXEL DECTRIS PILATUS3 6M 2018-11-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.9686 ESRF ID30B
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 3 47.1 98.89 0.0816 5.57 1.9 20658 76.83
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 3 3.1 98.89 0.4657 1.56
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 FREE R-VALUE 6R77 3 47.1 19646 981 97.11 0.22309 0.22109 0.2238 0.26182 0.26 RANDOM 79.52
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] 3.6 -6.52 2.91
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.324 r_dihedral_angle_4_deg 17.655 r_dihedral_angle_3_deg 15.987 r_scangle_other 10.63 r_mcangle_it 9.759 r_mcangle_other 9.759 r_dihedral_angle_1_deg 7.548 r_scbond_it 6.716 r_scbond_other 6.715 r_mcbond_it 6.338
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.324 r_dihedral_angle_4_deg 17.655 r_dihedral_angle_3_deg 15.987 r_scangle_other 10.63 r_mcangle_it 9.759 r_mcangle_other 9.759 r_dihedral_angle_1_deg 7.548 r_scbond_it 6.716 r_scbond_other 6.715 r_mcbond_it 6.338 r_mcbond_other 6.335 r_angle_refined_deg 1.397 r_angle_other_deg 1.202 r_chiral_restr 0.052 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5026 Nucleic Acid Atoms Solvent Atoms 1 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing