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Crystal Structure of Rv0047c from Mycobacterium tuberculosis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 295 0.1M Sodium Acetate, 1.8M Sodium Formate
Crystal Properties Matthews coefficient Solvent content 2.33 47.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.17 α = 90 b = 102.17 β = 90 c = 191.88 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 IMAGE PLATE RIGAKU RAXIS IV++ 2019-05-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.54178
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 3.15 30.08 90.7 0.99 22.1 12.9 17786
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.15 3.37 0.94
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 (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3.15 30.076 17735 856 90.457 0.207 0.2042 0.2526 0.2835 68.163
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] 24.963 24.963 -49.926
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.464 r_dihedral_angle_4_deg 20.429 r_dihedral_angle_3_deg 19.736 r_lrange_it 8.101 r_dihedral_angle_1_deg 5.835 r_scangle_it 4.642 r_mcangle_it 4.539 r_scbond_it 2.98 r_mcbond_it 2.829 r_angle_refined_deg 1.534
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.464 r_dihedral_angle_4_deg 20.429 r_dihedral_angle_3_deg 19.736 r_lrange_it 8.101 r_dihedral_angle_1_deg 5.835 r_scangle_it 4.642 r_mcangle_it 4.539 r_scbond_it 2.98 r_mcbond_it 2.829 r_angle_refined_deg 1.534 r_symmetry_xyhbond_nbd_refined 0.306 r_nbtor_refined 0.297 r_symmetry_nbd_refined 0.287 r_nbd_refined 0.239 r_ncsr_local_group_7 0.16 r_ncsr_local_group_1 0.159 r_ncsr_local_group_9 0.159 r_ncsr_local_group_8 0.155 r_ncsr_local_group_6 0.15 r_xyhbond_nbd_refined 0.149 r_ncsr_local_group_5 0.133 r_ncsr_local_group_10 0.129 r_ncsr_local_group_14 0.125 r_ncsr_local_group_12 0.123 r_ncsr_local_group_3 0.12 r_ncsr_local_group_2 0.118 r_ncsr_local_group_15 0.118 r_ncsr_local_group_13 0.116 r_chiral_restr 0.115 r_ncsr_local_group_11 0.115 r_ncsr_local_group_4 0.114 r_bond_refined_d 0.007 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6549 Nucleic Acid Atoms Solvent Atoms 12 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement Aimless data scaling iMOSFLM data reduction PHASER phasing