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Crystal structure of trans-3-Hydroxy-L-proline dehydratase in complex with substrate - closed conformation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1W61
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 Na HEPES 0.1 M, PEG 400, 2.0 Ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.69 54.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.415 α = 90 b = 106.547 β = 90 c = 149.456 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 PIXEL DECTRIS PILATUS3 S 6M 2018-02-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.9792 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 2 86.8 95.7 0.0774 5.2 1.9 59449
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 2 2.1 0.29
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 1W61 2 45.07 56179 2935 95.72 0.18937 0.18818 0.1975 0.21252 0.2195 RANDOM 30.299
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] 4.49 -0.69 -3.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.284 r_dihedral_angle_4_deg 15.475 r_dihedral_angle_3_deg 14.172 r_dihedral_angle_1_deg 7.508 r_long_range_B_refined 6.71 r_long_range_B_other 6.641 r_scangle_other 5.014 r_scbond_it 3.137 r_scbond_other 3.136 r_mcangle_it 2.909
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.284 r_dihedral_angle_4_deg 15.475 r_dihedral_angle_3_deg 14.172 r_dihedral_angle_1_deg 7.508 r_long_range_B_refined 6.71 r_long_range_B_other 6.641 r_scangle_other 5.014 r_scbond_it 3.137 r_scbond_other 3.136 r_mcangle_it 2.909 r_mcangle_other 2.909 r_mcbond_it 1.993 r_mcbond_other 1.992 r_angle_refined_deg 1.44 r_angle_other_deg 1.301 r_chiral_restr 0.064 r_bond_refined_d 0.008 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 5536 Nucleic Acid Atoms Solvent Atoms 397 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing