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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 sodium phosphate, PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.12 42.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.914 α = 90 b = 36.368 β = 90 c = 36.545 γ = 90
Symmetry Space Group P 21 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 100 CCD ADSC QUANTUM 315r 2017-12-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 0.979 SSRF BL17U1
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 2.1 54.96 93.4 0.074 20.35 8.6 8537
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 2.1 2.18 0.377
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 2.1 54.96 8031 475 93.41 0.20726 0.20421 0.2137 0.26573 0.2725 RANDOM 65.315
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] -0.12 0.1 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.3 r_dihedral_angle_3_deg 15.94 r_dihedral_angle_4_deg 13.356 r_long_range_B_refined 11.43 r_long_range_B_other 11.426 r_scangle_other 8.625 r_dihedral_angle_1_deg 7.135 r_mcangle_it 6.957 r_mcangle_other 6.952 r_scbond_it 6.009
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.3 r_dihedral_angle_3_deg 15.94 r_dihedral_angle_4_deg 13.356 r_long_range_B_refined 11.43 r_long_range_B_other 11.426 r_scangle_other 8.625 r_dihedral_angle_1_deg 7.135 r_mcangle_it 6.957 r_mcangle_other 6.952 r_scbond_it 6.009 r_scbond_other 5.666 r_mcbond_it 4.839 r_mcbond_other 4.832 r_angle_refined_deg 1.739 r_angle_other_deg 0.964 r_chiral_restr 0.104 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.003 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 1113 Nucleic Acid Atoms Solvent Atoms 18 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data scaling Coot model building HKL-2000 data reduction PHASER phasing