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Crystal Structure of ATP binding domain of PrrB from Mycobacterium Tuberculosis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YS3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 292 PEG750MME, Magnesium Chloride, Bis Tris Propane, glycerol, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 2.5 51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.047 α = 90 b = 61.047 β = 90 c = 208.429 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 MARRESEARCH 2004-07-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 0.887 EMBL/DESY, HAMBURG X11
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 1.78 88 99 0.054 27.6 6.9 41861 41427 -3 -3
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 1.78 1.81 99.8 0.862 2.5 6.6 2072
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1YS3 1.78 19.98 41861 39315 2088 99.22 0.203 0.2026 0.2003 0.1993 0.24595 0.2436 RANDOM 38.519
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 40.082 r_dihedral_angle_4_deg 17.474 r_dihedral_angle_3_deg 14.869 r_scangle_it 7.924 r_dihedral_angle_1_deg 5.67 r_scbond_it 5.079 r_mcangle_it 2.291 r_angle_refined_deg 1.821 r_mcbond_it 1.375 r_nbtor_refined 0.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.082 r_dihedral_angle_4_deg 17.474 r_dihedral_angle_3_deg 14.869 r_scangle_it 7.924 r_dihedral_angle_1_deg 5.67 r_scbond_it 5.079 r_mcangle_it 2.291 r_angle_refined_deg 1.821 r_mcbond_it 1.375 r_nbtor_refined 0.312 r_symmetry_hbond_refined 0.252 r_nbd_refined 0.212 r_xyhbond_nbd_refined 0.201 r_symmetry_vdw_refined 0.164 r_chiral_restr 0.132 r_bond_refined_d 0.019 r_gen_planes_refined 0.008 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2963 Nucleic Acid Atoms Solvent Atoms 167 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing