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High resolution crystal structure of Nitrogen Regulatory Protein (Rv2919c) of Mycobacterium tuberculosis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GNK PDB entry 1GNK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 290 0.1 M Immidazole, pH 6.5, 1.4 M Sodium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.39 48.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.149 α = 90 b = 77.149 β = 90 c = 51.84 γ = 120
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 Rosenbaum-Rock high-resolution double-crystal monochromator 2005-08-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.979 APS 19-ID
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 1.4 40.96 99.08 21338 21338
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 (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 MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1GNK 1.4 40.96 21338 21338 1131 99.08 0.2085 0.2085 0.20759 0.2065 0.22566 0.2227 RANDOM 16.443
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] -0.5 -0.25 -0.5 0.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.667 r_dihedral_angle_4_deg 14.392 r_dihedral_angle_3_deg 11.378 r_dihedral_angle_1_deg 5.107 r_scangle_it 2.286 r_scbond_it 1.378 r_angle_refined_deg 1.007 r_mcangle_it 0.92 r_mcbond_it 0.528 r_nbtor_refined 0.294
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.667 r_dihedral_angle_4_deg 14.392 r_dihedral_angle_3_deg 11.378 r_dihedral_angle_1_deg 5.107 r_scangle_it 2.286 r_scbond_it 1.378 r_angle_refined_deg 1.007 r_mcangle_it 0.92 r_mcbond_it 0.528 r_nbtor_refined 0.294 r_nbd_refined 0.192 r_symmetry_vdw_refined 0.142 r_symmetry_hbond_refined 0.09 r_chiral_restr 0.073 r_xyhbond_nbd_refined 0.063 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other 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 742 Nucleic Acid Atoms Solvent Atoms 136 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement ADSC data collection HKL-2000 data reduction HKL-2000 data scaling AMoRE phasing