☰ Navigation Tabs
Medium-chain dehydrogenase/reductase MrADH-WT
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3JV7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 289.2 Tris-HCl, PEG 4000
Crystal Properties Matthews coefficient Solvent content 3.76 67.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.12 α = 90 b = 96.12 β = 90 c = 199.02 γ = 120
Symmetry Space Group P 62 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 150 PIXEL Bruker PHOTON II multilayer 2023-03-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE BRUKER D8 QUEST 1.54178
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.59 43.28 100 0.176 0.076 13.1 11.8 17662
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.59 2.71 1.066 0.518
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.59 43.28 16819 843 99.93 0.19965 0.19757 0.2161 0.24041 0.2409 RANDOM 40.314
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] 1.28 0.64 1.28 -4.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.74 r_dihedral_angle_4_deg 16.594 r_dihedral_angle_3_deg 14.086 r_dihedral_angle_1_deg 5.913 r_long_range_B_refined 4.662 r_long_range_B_other 4.616 r_scangle_other 3.172 r_mcangle_other 2.486 r_mcangle_it 2.484 r_scbond_it 2.158
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.74 r_dihedral_angle_4_deg 16.594 r_dihedral_angle_3_deg 14.086 r_dihedral_angle_1_deg 5.913 r_long_range_B_refined 4.662 r_long_range_B_other 4.616 r_scangle_other 3.172 r_mcangle_other 2.486 r_mcangle_it 2.484 r_scbond_it 2.158 r_scbond_other 2.14 r_mcbond_it 1.534 r_mcbond_other 1.525 r_angle_refined_deg 1.354 r_angle_other_deg 0.77 r_chiral_restr 0.065 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 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 2479 Nucleic Acid Atoms Solvent Atoms 121 Heterogen Atoms 46
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction PROTEUM PLUS data reduction PROTEUM PLUS data scaling MOLREP phasing