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Crystal structure of conjugated polyketone reductase C2 from Candida Parapsilosis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VP5 PDB ENTRY 1VP5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.1 293 23% PEG 3350, 0.1M TRIS-HCL, pH 8.1, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.76 29.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.02 α = 90 b = 68.3 β = 90 c = 68.93 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 210 2008-11-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A Photon Factory AR-NW12A
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 1.7 20 99.8 0.044 28.91 29200
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 1VP5 1.7 19 29196 1482 99.9 0.189 0.187 0.1863 0.223 0.2216 RANDOM 20.97
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] -0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.031 r_dihedral_angle_4_deg 13.936 r_dihedral_angle_3_deg 13.344 r_dihedral_angle_1_deg 5.565 r_scangle_it 3.458 r_scbond_it 2.328 r_mcangle_it 1.549 r_angle_refined_deg 1.351 r_mcbond_it 0.908 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.031 r_dihedral_angle_4_deg 13.936 r_dihedral_angle_3_deg 13.344 r_dihedral_angle_1_deg 5.565 r_scangle_it 3.458 r_scbond_it 2.328 r_mcangle_it 1.549 r_angle_refined_deg 1.351 r_mcbond_it 0.908 r_nbtor_refined 0.305 r_nbd_refined 0.199 r_symmetry_vdw_refined 0.181 r_symmetry_hbond_refined 0.161 r_xyhbond_nbd_refined 0.147 r_chiral_restr 0.095 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 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 2385 Nucleic Acid Atoms Solvent Atoms 213 Heterogen Atoms
Software Software Software Name Purpose MOLREP phasing REFMAC refinement XDS data reduction XDS data scaling