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Structure of the peptidoglycan hydrolase RipB (Rv1478) from Mycobacterium tuberculosis at 1.6 resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HBW PDB ENTRY 2HBW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 293 0.2 M NaCl 0.1 M HEPES, 30% v/v PEG 400, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.07 59.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.98 α = 90 b = 92.98 β = 90 c = 53.192 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 CCD ADSC QUANTUM 315r MIRRORS 2009-10-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.6 40 92.3 0.066 0.066 19.1 7.4 32063 2.5 20.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.69 63.2 0.411 0.411 2.5 2.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 2HBW 1.6 40 2.5 32063 1604 92.3 0.161 0.159 0.1736 0.196 0.2077 RANDOM 19.26
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] -0.74 -0.37 -0.74 1.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.518 r_dihedral_angle_4_deg 19.803 r_dihedral_angle_3_deg 13.239 r_dihedral_angle_1_deg 6.277 r_scangle_it 4.646 r_scbond_it 2.909 r_mcangle_it 2.192 r_angle_refined_deg 2.076 r_mcbond_it 1.459 r_angle_other_deg 1.132
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.518 r_dihedral_angle_4_deg 19.803 r_dihedral_angle_3_deg 13.239 r_dihedral_angle_1_deg 6.277 r_scangle_it 4.646 r_scbond_it 2.909 r_mcangle_it 2.192 r_angle_refined_deg 2.076 r_mcbond_it 1.459 r_angle_other_deg 1.132 r_mcbond_other 0.47 r_chiral_restr 0.137 r_bond_refined_d 0.029 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1436 Nucleic Acid Atoms Solvent Atoms 242 Heterogen Atoms
Software Software Software Name Purpose DNA data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling