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Crystal structure of the PAS domain of nitrogen regulation protein NR(II) from Vibrio parahaemolyticus
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.5 289 0.1 M Sodium acetate, 3 M Sodium chloride, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.49 50.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.115 α = 90 b = 81.115 β = 90 c = 67.467 γ = 120
Symmetry Space Group P 63 2 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 315 2007-10-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97920 APS 19-ID
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 1.83 35.12 98.8 0.072 11.3 18.3 11960 11960 40.5
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 1.83 1.88 88.8 0.61 2.18 6.1 872
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 THROUGHOUT 1.83 35.12 11938 11938 566 98.77 0.1843 0.1843 0.1837 0.1825 0.1958 0.1967 RANDOM 33.354
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] 0.07 0.03 0.07 -0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 44.231 r_dihedral_angle_4_deg 19.435 r_dihedral_angle_3_deg 17.216 r_dihedral_angle_1_deg 6.496 r_scangle_it 3.449 r_scbond_it 2.279 r_mcangle_it 1.974 r_angle_refined_deg 1.78 r_mcbond_it 1.194 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 44.231 r_dihedral_angle_4_deg 19.435 r_dihedral_angle_3_deg 17.216 r_dihedral_angle_1_deg 6.496 r_scangle_it 3.449 r_scbond_it 2.279 r_mcangle_it 1.974 r_angle_refined_deg 1.78 r_mcbond_it 1.194 r_nbtor_refined 0.306 r_symmetry_vdw_refined 0.29 r_nbd_refined 0.224 r_xyhbond_nbd_refined 0.193 r_chiral_restr 0.136 r_symmetry_hbond_refined 0.101 r_bond_refined_d 0.016 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 838 Nucleic Acid Atoms Solvent Atoms 69 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction SBC-Collect data collection HKL-3000 data reduction SHELXD phasing MLPHARE phasing DM phasing SOLVE phasing RESOLVE phasing HKL-3000 phasing