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Crystal structure of conjugated polyketone reductase C2 from candida parapsilosis complexed with NADPH
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3AFY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.4 293 2MM NADPH, 0.1M TRIS-HCL, 25% PEG 3350, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.85 33.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.21 α = 90 b = 127.45 β = 108.99 c = 46.44 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 100 CCD ADSC QUANTUM 270 2009-11-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NE3A Photon Factory AR-NE3A
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 1.8 20 99.2 0.036 23.34 46639
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 3AFY 1.8 19.51 46638 2359 99.4 0.175 0.172 0.169 0.222 0.2193 RANDOM 22.76
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.953 r_dihedral_angle_4_deg 18.856 r_dihedral_angle_3_deg 15.11 r_dihedral_angle_1_deg 6.009 r_scangle_it 4.827 r_scbond_it 3.099 r_mcangle_it 1.953 r_angle_refined_deg 1.946 r_mcbond_it 1.198 r_chiral_restr 0.136
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.953 r_dihedral_angle_4_deg 18.856 r_dihedral_angle_3_deg 15.11 r_dihedral_angle_1_deg 6.009 r_scangle_it 4.827 r_scbond_it 3.099 r_mcangle_it 1.953 r_angle_refined_deg 1.946 r_mcbond_it 1.198 r_chiral_restr 0.136 r_bond_refined_d 0.022 r_gen_planes_refined 0.011 r_bond_other_d r_angle_other_deg 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4801 Nucleic Acid Atoms Solvent Atoms 257 Heterogen Atoms 96
Software Software Software Name Purpose MOLREP phasing REFMAC refinement XDS data reduction XDS data scaling