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NH3-dependent NAD synthetase from Campylobacter jejuni subsp. jejuni NCTC 11168 in complex with the nitrate ion
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XNH PDB entry 1XNH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 295 4.25 M NaNitrate, 0.1 M Bis-Tris, 10 mM NAD, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 3.45 64.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.945 α = 90 b = 120.945 β = 90 c = 91.795 γ = 120
Symmetry Space Group P 3 2 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 CCD MARMOSAIC 300 mm CCD MIRROR 2010-07-31 M MOLECULAR REPLACEMENT
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97857 APS 21-ID-G
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 2.74 30 100 0.076 23.2 7.6 20690 20690 -3 74
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) 2.74 2.8 100 0.882 2.3 7.7 1029
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 PDB entry 1XNH 2.74 30 19563 19563 1056 99.21 0.21084 0.20911 0.2098 0.24451 0.2416 RANDOM 72.083
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] 1.27 0.64 1.27 -1.91
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.761 r_dihedral_angle_4_deg 20.196 r_dihedral_angle_3_deg 19.143 r_dihedral_angle_1_deg 5.218 r_scangle_it 4.636 r_scbond_it 2.97 r_angle_refined_deg 1.653 r_mcangle_it 1.475 r_mcbond_it 0.72 r_chiral_restr 0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.761 r_dihedral_angle_4_deg 20.196 r_dihedral_angle_3_deg 19.143 r_dihedral_angle_1_deg 5.218 r_scangle_it 4.636 r_scbond_it 2.97 r_angle_refined_deg 1.653 r_mcangle_it 1.475 r_mcbond_it 0.72 r_chiral_restr 0.11 r_bond_refined_d 0.016 r_gen_planes_refined 0.005 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3577 Nucleic Acid Atoms Solvent Atoms 65 Heterogen Atoms 16
Software Software Software Name Purpose Blu-Ice data collection PHENIX model building CCP4 model building MrBUMP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing CCP4 phasing