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Crystal structure of 15-hydroxyprostaglandin dehydrogenase type1, complexed with NAD+
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1WMB PDB ENTRY 1WMB, 1IY8, 1ZK3 experimental model PDB 1IY8 PDB ENTRY 1WMB, 1IY8, 1ZK3 experimental model PDB 1ZK3 PDB ENTRY 1WMB, 1IY8, 1ZK3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 298 0.1 PCB, 30% PEG 1000, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 2.06 40.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.54 α = 90 b = 49.54 β = 90 c = 195.771 γ = 90
Symmetry Space Group P 41 21 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 IMAGE PLATE RIGAKU RAXIS IV OSMIC M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.65 196.12 99.6 0.077 0.077 23.9 11.9 30422 30422
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.65 1.74 99.6 0.688 0.688 2.5 7.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1WMB, 1IY8, 1ZK3 1.65 21.86 28883 28883 1538 99.4 0.17746 0.17746 0.17568 0.1704 0.21214 0.209 RANDOM 18.567
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] 0.38 0.38 -0.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.233 r_dihedral_angle_4_deg 20.858 r_dihedral_angle_3_deg 12.522 r_dihedral_angle_1_deg 5.284 r_scangle_it 3.736 r_scbond_it 2.482 r_angle_refined_deg 1.627 r_mcangle_it 1.489 r_mcbond_it 1.054 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.233 r_dihedral_angle_4_deg 20.858 r_dihedral_angle_3_deg 12.522 r_dihedral_angle_1_deg 5.284 r_scangle_it 3.736 r_scbond_it 2.482 r_angle_refined_deg 1.627 r_mcangle_it 1.489 r_mcbond_it 1.054 r_nbtor_refined 0.304 r_nbd_refined 0.205 r_symmetry_vdw_refined 0.185 r_xyhbond_nbd_refined 0.141 r_symmetry_hbond_refined 0.119 r_chiral_restr 0.111 r_bond_refined_d 0.019 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2026 Nucleic Acid Atoms Solvent Atoms 299 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling PHASER phasing