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Trans-3/4-proline-hydroxylase H11 with 4-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 7 289.15 0.7M Sodium citrate tribasic dihydrate and 0.1M Bis-Tris propane (pH 7.0)
Crystal Properties Matthews coefficient Solvent content 3.43 64.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.289 α = 90 b = 75.289 β = 90 c = 144.544 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 2019-10-24 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) CC (Half) 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 1.84 75.29 99.9 0.058 0.059 0.012 1 152.6 24.4 36880
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 1.84 1.87 100 0.529 0.54 0.107 0.97 7.8 25.1
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 1.84 24.63 34875 1952 99.84 0.1509 0.1491 0.1624 0.1819 0.1937 RANDOM 36.834
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] 0.22 0.22 -0.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 14.587 r_dihedral_angle_3_deg 12.504 r_dihedral_angle_1_deg 6.493 r_rigid_bond_restr 4.91 r_angle_refined_deg 0.939 r_angle_other_deg 0.344 r_chiral_restr 0.05 r_gen_planes_refined 0.004 r_bond_refined_d 0.003 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 14.587 r_dihedral_angle_3_deg 12.504 r_dihedral_angle_1_deg 6.493 r_rigid_bond_restr 4.91 r_angle_refined_deg 0.939 r_angle_other_deg 0.344 r_chiral_restr 0.05 r_gen_planes_refined 0.004 r_bond_refined_d 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2094 Nucleic Acid Atoms Solvent Atoms 164 Heterogen Atoms 9
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling PHASER phasing