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Crystal structure of zebrafish prostacyclin synthase (cytochrome P450 8A1) in complex with substrate analog U51605
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2IAG PDB ENTRY 2IAG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 Soaking 7.5 277 The crystal of prostacyclin synthase-U51605 complex was prepared by soaking the ligand-free crystals in 2 microliter of substitute mother liquor (23% PEG 3350, 50mM HEPES (Na-salt; pH 7.5)) containing 0.25mM of U51605 for a week, Soaking, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.23 44.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.47 α = 90 b = 88.044 β = 90 c = 190.142 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 CCD ADSC QUANTUM 315 Toroidal FM 2007-04-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL13B1 1.0 NSRRC BL13B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.5 30 92.3 0.064 12.9 4.7 35343 32622 1 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.59 94.2 0.302 2.8 4.4 3269
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) 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 2IAG 2.5 27.75 1 1 35343 30957 1643 91.58 0.21817 0.218 0.21414 0.2075 0.29209 0.2824 RANDOM 32.075
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] -0.39 -0.44 0.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.455 r_dihedral_angle_3_deg 18.059 r_dihedral_angle_4_deg 18.031 r_dihedral_angle_1_deg 5.472 r_mcangle_it 2.913 r_scangle_it 2.754 r_scbond_it 1.895 r_mcbond_it 1.856 r_angle_refined_deg 1.404 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.455 r_dihedral_angle_3_deg 18.059 r_dihedral_angle_4_deg 18.031 r_dihedral_angle_1_deg 5.472 r_mcangle_it 2.913 r_scangle_it 2.754 r_scbond_it 1.895 r_mcbond_it 1.856 r_angle_refined_deg 1.404 r_nbtor_refined 0.306 r_nbd_refined 0.206 r_symmetry_hbond_refined 0.196 r_xyhbond_nbd_refined 0.153 r_symmetry_vdw_refined 0.153 r_chiral_restr 0.09 r_bond_refined_d 0.009 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6991 Nucleic Acid Atoms Solvent Atoms 223 Heterogen Atoms 230
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling PHASER phasing