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Structural characterization of mutated NreA protein in nitrate binding site from Staphylococcus aureus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4PAU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 295.15 K/Na tartrate, Imidazole, NaCl
Crystal Properties Matthews coefficient Solvent content 2.8 56.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.072 α = 90 b = 38.782 β = 91.57 c = 70.574 γ = 90
Symmetry Space Group P 1 21 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 DECTRIS PILATUS3 S 6M 2018-01-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.978 SSRF BL18U1
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 2.29 70.55 95.8 0.09 13.7 4 16671
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 2.3 2.38 0.294
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 4PAU 2.29 70.55 15916 747 95.82 0.19104 0.18849 0.194 0.24561 0.2423 RANDOM 61.017
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] 0.13 -0.39 -0.02 -0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.376 r_dihedral_angle_3_deg 14.539 r_dihedral_angle_4_deg 12.13 r_long_range_B_refined 11.027 r_long_range_B_other 11.025 r_scangle_other 8.878 r_mcangle_other 6.709 r_mcangle_it 6.699 r_dihedral_angle_1_deg 6.388 r_scbond_it 6.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.376 r_dihedral_angle_3_deg 14.539 r_dihedral_angle_4_deg 12.13 r_long_range_B_refined 11.027 r_long_range_B_other 11.025 r_scangle_other 8.878 r_mcangle_other 6.709 r_mcangle_it 6.699 r_dihedral_angle_1_deg 6.388 r_scbond_it 6.003 r_scbond_other 6.001 r_mcbond_it 4.885 r_mcbond_other 4.836 r_angle_refined_deg 1.762 r_angle_other_deg 0.989 r_chiral_restr 0.106 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 2286 Nucleic Acid Atoms Solvent Atoms 33 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data scaling PHASER phasing HKL-2000 data reduction