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Pinoresinol hydroxylase from Pseudomonas sp.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 Morpheus H5
Crystal Properties Matthews coefficient Solvent content 2.04 39.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.214 α = 90 b = 131.809 β = 90 c = 137.458 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 EIGER X 16M 2023-11-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.965460 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.8 59.43 98.7 0.06 0.998 12.6 4.1 93635
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.83 0.389
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.8 51.76 88842 4743 98.06 0.18849 0.1864 0.22772 0.2104 RANDOM
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] 1.74 0.2 -1.95
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 6.858 r_long_range_B_other 6.855 r_scangle_other 5.172 r_mcangle_it 3.894 r_mcangle_other 3.894 r_scbond_it 3.406 r_scbond_other 3.405 r_mcbond_it 2.775 r_mcbond_other 2.774 r_bond_refined_d
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 6.858 r_long_range_B_other 6.855 r_scangle_other 5.172 r_mcangle_it 3.894 r_mcangle_other 3.894 r_scbond_it 3.406 r_scbond_other 3.405 r_mcbond_it 2.775 r_mcbond_other 2.774 r_bond_refined_d r_bond_other_d r_angle_refined_deg r_angle_other_deg r_dihedral_angle_1_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_chiral_restr r_gen_planes_refined r_gen_planes_other 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 8510 Nucleic Acid Atoms Solvent Atoms 369 Heterogen Atoms 117
Software Software Software Name Purpose XDS data reduction PHENIX model building REFMAC refinement Aimless data scaling