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RipD (Rv1566c) from Mycobacterium tuberculosis: a non-catalytic NlpC/p60 domain protein with two penta-peptide repeat units (PVQQA-PVQPA)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.9 293 0.1M Tris/HCl pH 7.9, 0.2M Trimethylamine N-oxide, 20% PEG 2000 MME, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.12 42.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.247 α = 90 b = 30.752 β = 120.85 c = 61.921 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 CCD MARMOSAIC 225 mm CCD 2013-06-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.873 ESRF ID23-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.17 53.16 99.3 43924 43616 2 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.17 1.69 96.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) Number Reflections (All) 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 1.17 53.16 2 2 43924 41701 2221 99.32 0.14773 0.14672 0.1564 0.16648 0.1723 RANDOM 11.969
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] -0.1 -0.07 0.21 -0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.489 r_sphericity_free 25.397 r_dihedral_angle_4_deg 19.215 r_dihedral_angle_3_deg 13.315 r_sphericity_bonded 8.417 r_dihedral_angle_1_deg 6.068 r_rigid_bond_restr 3.105 r_angle_refined_deg 1.441 r_angle_other_deg 0.93 r_chiral_restr 0.093
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.489 r_sphericity_free 25.397 r_dihedral_angle_4_deg 19.215 r_dihedral_angle_3_deg 13.315 r_sphericity_bonded 8.417 r_dihedral_angle_1_deg 6.068 r_rigid_bond_restr 3.105 r_angle_refined_deg 1.441 r_angle_other_deg 0.93 r_chiral_restr 0.093 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 997 Nucleic Acid Atoms Solvent Atoms 139 Heterogen Atoms
Software Software Software Name Purpose DNA data collection MOLREP phasing REFMAC refinement SCALA data scaling