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Short-chain dehydrogenase from Sphingobium yanoikuyae in complex with NADPH
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3P19 PDB ENTRY 3P19
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.5 0.1M MES BUFFER PH 5.5 WITH 0.3 M SODIUM ACETATE AND 15% (W/V) PEG 4K, WITH A PROTEIN CONCENTRATION OF 20 MG ML-1. CRYSTALS WERE SOAKED WITH 10 MM NADPH FOR 5 MIN
Crystal Properties Matthews coefficient Solvent content 3.2 62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 144.91 α = 90 b = 86.84 β = 106.36 c = 155.61 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 120 2012-12-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 Diamond I02
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.5 139 99.7 0.14 8.2 4.2 133601 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.56 99.8 0.54 3 4.3
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 PDB ENTRY 3P19 2.5 139.04 121980 6490 99.76 0.23472 0.23388 0.2409 0.25055 0.2585 RANDOM 35.145
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] -2.63 0.48 -2.07 3.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.534 r_dihedral_angle_4_deg 16.594 r_dihedral_angle_3_deg 14.971 r_dihedral_angle_1_deg 6.025 r_mcangle_it 3.728 r_scbond_it 2.7 r_mcbond_it 2.473 r_mcbond_other 2.473 r_angle_refined_deg 1.604 r_angle_other_deg 1.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.534 r_dihedral_angle_4_deg 16.594 r_dihedral_angle_3_deg 14.971 r_dihedral_angle_1_deg 6.025 r_mcangle_it 3.728 r_scbond_it 2.7 r_mcbond_it 2.473 r_mcbond_other 2.473 r_angle_refined_deg 1.604 r_angle_other_deg 1.16 r_chiral_restr 0.084 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_bond_other_d 0.008 r_gen_planes_other 0.006 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 18922 Nucleic Acid Atoms Solvent Atoms 290 Heterogen Atoms 480
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling BALBES phasing