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M.tuberculosis nitrobindin with a water molecule coordinated to the heme iron atom
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2FR2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 294 0.2 M MgCl2, 0.1 M Tris, PEG 4k 30%
Crystal Properties Matthews coefficient Solvent content 2.39 48.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.782 α = 90 b = 74.295 β = 90 c = 80.339 γ = 90
Symmetry Space Group I 2 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 PIXEL DECTRIS PILATUS3 X 2M 2018-06-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.9 ESRF ID23-2
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 1.2 48.5 95 8.7 12.4 54078
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.2 1.26 74.3 2.5 10.2
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 2fr2 1.2 47.09 51392 2685 94.76 0.14157 0.13978 0.1397 0.17578 0.1753 RANDOM 12.814
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] -0.1 -0.04 0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.663 r_sphericity_free 24.936 r_dihedral_angle_4_deg 18.508 r_dihedral_angle_3_deg 11.623 r_sphericity_bonded 10.329 r_dihedral_angle_1_deg 8.95 r_rigid_bond_restr 4.825 r_long_range_B_refined 3.815 r_long_range_B_other 3.444 r_scangle_other 2.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.663 r_sphericity_free 24.936 r_dihedral_angle_4_deg 18.508 r_dihedral_angle_3_deg 11.623 r_sphericity_bonded 10.329 r_dihedral_angle_1_deg 8.95 r_rigid_bond_restr 4.825 r_long_range_B_refined 3.815 r_long_range_B_other 3.444 r_scangle_other 2.98 r_scbond_it 2.42 r_scbond_other 2.389 r_mcangle_other 2.173 r_mcangle_it 2.067 r_mcbond_it 1.723 r_mcbond_other 1.474 r_angle_refined_deg 1.359 r_angle_other_deg 0.962 r_chiral_restr 0.073 r_gen_planes_refined 0.034 r_gen_planes_other 0.027 r_bond_refined_d 0.012 r_bond_other_d 0.001 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1224 Nucleic Acid Atoms Solvent Atoms 219 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing