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Crystal structure of the Vitamin B3 transporter PnuC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 15% PEG3350, 0.1 M Succinic Acid, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.74 67.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.32 α = 90 b = 112.93 β = 90 c = 120.37 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 PIXEL DECTRIS PILATUS 2M 2014-06-27 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 0.9794, 0.9800, 0.972 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 50 99.8 31993 31933
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.9 100 3134
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT 2.8 48.31 31993 30336 1597 99.81 0.24554 0.24554 0.24392 0.2452 0.27582 0.2764 RANDOM 117.737
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] 0.14 4.37 -4.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.608 r_dihedral_angle_3_deg 22.426 r_dihedral_angle_4_deg 20.626 r_long_range_B_refined 11.534 r_dihedral_angle_1_deg 7.044 r_mcangle_it 6.378 r_scbond_it 4.769 r_mcbond_it 3.983 r_angle_refined_deg 1.219 r_chiral_restr 0.095
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.608 r_dihedral_angle_3_deg 22.426 r_dihedral_angle_4_deg 20.626 r_long_range_B_refined 11.534 r_dihedral_angle_1_deg 7.044 r_mcangle_it 6.378 r_scbond_it 4.769 r_mcbond_it 3.983 r_angle_refined_deg 1.219 r_chiral_restr 0.095 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5674 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 134
Software Software Software Name Purpose DA+ data collection PHENIX model building REFMAC refinement XDS data reduction XDS data scaling PHENIX phasing