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Crystal Structure of Polyneuridine Aldehyde Esterase Complexed with 16-epi-Vellosimine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2WFL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.3 296 PEG 3350, 0.20M Bis-Tris, 0.25M Lis2SO4, pH 6.3, vapor diffusion, hanging drop, temperature 296K
Crystal Properties Matthews coefficient Solvent content 2.3 46.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 171.21 α = 90 b = 44.61 β = 104.44 c = 180.41 γ = 90
Symmetry Space Group C 1 2 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 PIXEL PSI PILATUS 6M 2007-11-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.000 SLS X06SA
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 2.19 20 97.2 0.077 0.077 10.9 3.2 66881 66881 44.6
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) 2.19 2.32 93.9 0.425 0.425 2.2 3 10364
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2WFL 2.19 20 66881 66881 3407 97.19 0.212 0.212 0.209 0.278 0.2898 RANDOM 27.852
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] -2.05 0.61 3.26 -0.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.778 r_dihedral_angle_3_deg 18.159 r_dihedral_angle_4_deg 16.221 r_dihedral_angle_1_deg 6.814 r_scangle_it 3.613 r_scbond_it 2.491 r_angle_refined_deg 1.841 r_mcangle_it 1.427 r_mcbond_it 0.923 r_symmetry_vdw_refined 0.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.778 r_dihedral_angle_3_deg 18.159 r_dihedral_angle_4_deg 16.221 r_dihedral_angle_1_deg 6.814 r_scangle_it 3.613 r_scbond_it 2.491 r_angle_refined_deg 1.841 r_mcangle_it 1.427 r_mcbond_it 0.923 r_symmetry_vdw_refined 0.36 r_symmetry_hbond_refined 0.337 r_nbtor_refined 0.316 r_nbd_refined 0.237 r_xyhbond_nbd_refined 0.177 r_chiral_restr 0.128 r_bond_refined_d 0.018 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9985 Nucleic Acid Atoms Solvent Atoms 245 Heterogen Atoms 88
Software Software Software Name Purpose MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XDS data scaling