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Rv0394c protein from Mycobacterium tuberculosis H37Rv (C49A mutant)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold Locally prepared
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4 289 Protein at 10 mg/ml mixed 1:1 with mother liquor of 2M NaCl, 0.1M sodium citrate, pH 4.0, 20% PEG 6000
Crystal Properties Matthews coefficient Solvent content 4.3 71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 139.377 α = 90 b = 139.377 β = 90 c = 139.377 γ = 90
Symmetry Space Group I 21 3
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 EIGER R 4M 2024-03-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-X 1.54179
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 3.05 34.84 99.9 0.16 0.162 0.025 1 21.6 40.4 8746 138.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.05 3.26 100 5.341 5.407 0.837 0.242 1 41.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 3.05 32.87 7441 346 88.93 0.22275 0.22144 0.2233 0.25153 0.2344 RANDOM 151.532
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.738 r_dihedral_angle_4_deg 20.251 r_dihedral_angle_3_deg 17.592 r_long_range_B_refined 16.086 r_scangle_it 10.381 r_mcangle_it 7.807 r_scbond_it 6.152 r_dihedral_angle_1_deg 5.839 r_mcbond_it 4.518 r_angle_refined_deg 0.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.738 r_dihedral_angle_4_deg 20.251 r_dihedral_angle_3_deg 17.592 r_long_range_B_refined 16.086 r_scangle_it 10.381 r_mcangle_it 7.807 r_scbond_it 6.152 r_dihedral_angle_1_deg 5.839 r_mcbond_it 4.518 r_angle_refined_deg 0.93 r_nbtor_refined 0.301 r_symmetry_vdw_refined 0.259 r_symmetry_hbond_refined 0.222 r_nbd_refined 0.2 r_xyhbond_nbd_refined 0.135 r_chiral_restr 0.069 r_bond_refined_d 0.003 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1421 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PDB_EXTRACT data extraction PHASER phasing