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Trans-3/4-proline-hydroxylase H11 with AKG and L-proline
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 289.15 0.7M Sodium citrate tribasic dihydrate and 0.1M Bis-Tris propane (pH 7.0)
Crystal Properties Matthews coefficient Solvent content 3.4 63.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.437 α = 90 b = 106.437 β = 90 c = 145.016 γ = 90
Symmetry Space Group P 41 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 CCD ADSC QUANTUM 315r 2017-06-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.979 SSRF BL17U
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.139 85.81 94.46 0.132 0.135 0.025 8.3 28.6 44086
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.14 2.18 99 0.529 0.538 0.1 0.981 1.3
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 6LNS 2.14 39.79 41919 2167 94.48 0.15547 0.15234 0.1663 0.21603 0.2256 RANDOM 36.658
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] -0.13 -0.13 0.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 15.517 r_dihedral_angle_3_deg 15.293 r_long_range_B_refined 8.491 r_long_range_B_other 8.491 r_scangle_other 8.118 r_mcangle_it 7.786 r_mcangle_other 7.785 r_scbond_it 7.44 r_scbond_other 7.438 r_dihedral_angle_1_deg 6.974
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 15.517 r_dihedral_angle_3_deg 15.293 r_long_range_B_refined 8.491 r_long_range_B_other 8.491 r_scangle_other 8.118 r_mcangle_it 7.786 r_mcangle_other 7.785 r_scbond_it 7.44 r_scbond_other 7.438 r_dihedral_angle_1_deg 6.974 r_mcbond_it 6.377 r_mcbond_other 6.376 r_rigid_bond_restr 4.482 r_angle_refined_deg 1.268 r_angle_other_deg 0.436 r_chiral_restr 0.06 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4215 Nucleic Acid Atoms Solvent Atoms 291 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing