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Crystal structure of human Nicotinic Acid Phosphoribosyltransferase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2F7F
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277 0.1 M Sodium cacodylate pH 6.5 and 1.7 M Sodium acetate
Crystal Properties Matthews coefficient Solvent content 2.42 49.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.018 α = 90 b = 101.091 β = 90 c = 125.144 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 MARMOSAIC 225 mm CCD 2013-07-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.972 ESRF ID23-2
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 2.9 58.64 99.7 0.011 10 4.4 25261
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.9 99.3 0.037 3.7 4.2
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 2F7F 2.9 50 25137 124 99.48 0.19711 0.19689 0.2054 0.24285 0.265 RANDOM 41.616
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] -1.23 4.24 -3.01
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 11.955 r_long_range_B_other 11.951 r_mcangle_it 6.346 r_mcangle_other 6.346 r_scangle_other 6.245 r_mcbond_it 3.691 r_mcbond_other 3.691 r_scbond_it 3.563 r_scbond_other 3.562 r_angle_refined_deg 1.832
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 11.955 r_long_range_B_other 11.951 r_mcangle_it 6.346 r_mcangle_other 6.346 r_scangle_other 6.245 r_mcbond_it 3.691 r_mcbond_other 3.691 r_scbond_it 3.563 r_scbond_other 3.562 r_angle_refined_deg 1.832 r_angle_other_deg 1.021 r_chiral_restr 0.156 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_dihedral_angle_1_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg 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 7558 Nucleic Acid Atoms Solvent Atoms 98 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MR-Rosetta phasing SCALA data scaling XDS data reduction XDS data scaling