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Crystal structure of PfaD from Shewanella oneidensis in complex with NAD+ determined by in-situ diffraction.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4YX6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 298 0.2 M potassium/sodium tartate, 0.1 M Bis tris propane at pH 8.5 and 20 % (w/v) polyethylene glycol.
Crystal Properties Matthews coefficient Solvent content 2.59 52.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.68 α = 90 b = 106.68 β = 90 c = 217.477 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 298 PIXEL DECTRIS PILATUS 6M 2013-10-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.9686 Diamond I24
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 2.8 48.44 95.9 0.278 9.6 4.7 30357 9.6
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 4YX6 2.8 48.44 28792 1477 95.33 0.21418 0.2122 0.2138 0.2527 0.2503 RANDOM 32.51
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] 1.26 1.26 -2.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.986 r_dihedral_angle_4_deg 18.522 r_dihedral_angle_3_deg 16.312 r_long_range_B_refined 6.491 r_long_range_B_other 6.491 r_scangle_other 4.504 r_dihedral_angle_1_deg 4.12 r_mcangle_other 3.944 r_mcangle_it 3.943 r_scbond_it 2.806
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.986 r_dihedral_angle_4_deg 18.522 r_dihedral_angle_3_deg 16.312 r_long_range_B_refined 6.491 r_long_range_B_other 6.491 r_scangle_other 4.504 r_dihedral_angle_1_deg 4.12 r_mcangle_other 3.944 r_mcangle_it 3.943 r_scbond_it 2.806 r_scbond_other 2.806 r_mcbond_it 2.439 r_mcbond_other 2.437 r_angle_refined_deg 0.805 r_angle_other_deg 0.583 r_chiral_restr 0.044 r_bond_refined_d 0.003 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7315 Nucleic Acid Atoms Solvent Atoms 60 Heterogen Atoms 150
Software Software Software Name Purpose REFMAC refinement PHASER phasing Coot model building XDS data reduction Aimless data scaling