☰ Navigation Tabs
Crystal Structure of the Class Ib Ribonucleotide Reductase R2F-2 subunit from Mycobacterium tuberculosis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1R2F PDB ENTRY 1R2F
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.6 0.6 M AMSO4, 100MM NACT PH 5.6, 50MM NA/K TARTRATE
Crystal Properties Matthews coefficient Solvent content 3.4 63.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 161.492 α = 90 b = 161.492 β = 90 c = 115.53 γ = 90
Symmetry Space Group P 42 21 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 CCD ADSC CCD 2003-08-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.2 40 99 0.091 10 4.84 77125
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 2.2 2.25 93.5 0.445 1.7
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 PDB ENTRY 1R2F 2.2 111.8 73204 3870 98.9 0.177 0.175 0.1833 0.202 0.21 RANDOM 28.39
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] -0.55 -0.55 1.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.974 r_scangle_it 5.35 r_scbond_it 3.191 r_mcangle_it 1.947 r_angle_refined_deg 1.85 r_mcbond_it 1.013 r_angle_other_deg 0.973 r_symmetry_vdw_other 0.355 r_nbd_other 0.234 r_nbd_refined 0.232
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.974 r_scangle_it 5.35 r_scbond_it 3.191 r_mcangle_it 1.947 r_angle_refined_deg 1.85 r_mcbond_it 1.013 r_angle_other_deg 0.973 r_symmetry_vdw_other 0.355 r_nbd_other 0.234 r_nbd_refined 0.232 r_symmetry_hbond_refined 0.197 r_xyhbond_nbd_refined 0.166 r_symmetry_vdw_refined 0.132 r_chiral_restr 0.12 r_nbtor_other 0.094 r_metal_ion_refined 0.077 r_bond_refined_d 0.023 r_gen_planes_refined 0.01 r_gen_planes_other 0.008 r_bond_other_d 0.002 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_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_refined 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 6905 Nucleic Acid Atoms Solvent Atoms 391 Heterogen Atoms 63
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing