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Structure of Rv0455c from Mycobacterium tuberculosis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8DQY 8DQY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 35 % Tacsimate pH 7.0
Crystal Properties Matthews coefficient Solvent content 1.8 31.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.039 α = 90 b = 25.228 β = 104.246 c = 58.631 γ = 90
Symmetry Space Group C 1 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 PIXEL DECTRIS PILATUS 6M 2022-03-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.97946 SSRL BL12-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 1.8 33.966 97.8 0.968 7.7 3.4 9253
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 1.8 1.84 0.614
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 8DQY 1.8 33.966 9250 543 97.409 0.16 0.1572 0.1721 0.2109 0.2265 27.549
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] 1.409 1.632 -1.967 -0.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.556 r_dihedral_angle_2_deg 14.88 r_dihedral_angle_3_deg 14.083 r_lrange_it 7.232 r_lrange_other 7.195 r_dihedral_angle_1_deg 6.793 r_scangle_it 4.782 r_scangle_other 4.779 r_mcangle_other 3.669 r_mcangle_it 3.663
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.556 r_dihedral_angle_2_deg 14.88 r_dihedral_angle_3_deg 14.083 r_lrange_it 7.232 r_lrange_other 7.195 r_dihedral_angle_1_deg 6.793 r_scangle_it 4.782 r_scangle_other 4.779 r_mcangle_other 3.669 r_mcangle_it 3.663 r_scbond_it 3.048 r_scbond_other 3.045 r_mcbond_it 2.399 r_mcbond_other 2.32 r_angle_refined_deg 1.38 r_angle_other_deg 0.477 r_xyhbond_nbd_refined 0.226 r_nbd_refined 0.221 r_nbd_other 0.205 r_nbtor_refined 0.194 r_symmetry_nbd_other 0.193 r_symmetry_xyhbond_nbd_refined 0.18 r_symmetry_nbd_refined 0.149 r_chiral_restr 0.072 r_symmetry_nbtor_other 0.072 r_gen_planes_refined 0.008 r_bond_refined_d 0.006 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 970 Nucleic Acid Atoms Solvent Atoms 91 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing