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Trans-3/4-proline-hydroxylase H11 with 3-hydroxyl-proline
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6LNS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 0.7 289.15 0.7M Sodium citrate tribasic dihydrate, 0.1M Bis-Tris propane (pH 7.0)
Crystal Properties Matthews coefficient Solvent content 3.42 64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.39 α = 90 b = 75.39 β = 90 c = 143.65 γ = 90
Symmetry Space Group P 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 PIXEL DECTRIS EIGER X 16M 2019-12-10 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 2.38 75.39 99.9 0.067 0.07 0.02 86.4 12.6 17231
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 2.38 2.42 100 0.502 0.521 0.141 0.969 10.3 13.2
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 2.38 75.39 16341 854 99.79 0.1933 0.1916 0.1998 0.2255 0.2314 RANDOM 50.263
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] 0.01 0.01 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.598 r_dihedral_angle_4_deg 18.366 r_dihedral_angle_3_deg 17.799 r_dihedral_angle_1_deg 7.814 r_angle_refined_deg 1.898 r_angle_other_deg 1.099 r_chiral_restr 0.118 r_bond_refined_d 0.018 r_gen_planes_refined 0.01 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.598 r_dihedral_angle_4_deg 18.366 r_dihedral_angle_3_deg 17.799 r_dihedral_angle_1_deg 7.814 r_angle_refined_deg 1.898 r_angle_other_deg 1.099 r_chiral_restr 0.118 r_bond_refined_d 0.018 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2059 Nucleic Acid Atoms Solvent Atoms 24 Heterogen Atoms 9
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling PHASER phasing