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Crystal structure of DacB from Streptococcus pneumoniae D39
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8 0.01 M ZINC CHLORIDE, 0.1 M TRIS-HCL PH 8.0, 14% (W/V) PEG 6000
Crystal Properties Matthews coefficient Solvent content 2.29 46.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.95 α = 90 b = 37.634 β = 97.98 c = 102.837 γ = 90
Symmetry Space Group P 1 21 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 PIXEL DECTRIS PILATUS 6M M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 Diamond I03
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 50.92 99.7 0.18 8.2 6.7 26483 2.3
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 2 2.05 99.2 0.8 2.3 6.6
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2 101.84 25196 1276 99.56 0.18409 0.18114 0.24263 0.2236 RANDOM 24.168
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] 1.97 0.55 -0.9 -1.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.669 r_dihedral_angle_4_deg 18.113 r_dihedral_angle_3_deg 14.692 r_dihedral_angle_1_deg 6.616 r_scbond_it 3.158 r_mcangle_it 2.82 r_angle_refined_deg 1.888 r_mcbond_it 1.818 r_mcbond_other 1.815 r_angle_other_deg 1.146
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.669 r_dihedral_angle_4_deg 18.113 r_dihedral_angle_3_deg 14.692 r_dihedral_angle_1_deg 6.616 r_scbond_it 3.158 r_mcangle_it 2.82 r_angle_refined_deg 1.888 r_mcbond_it 1.818 r_mcbond_other 1.815 r_angle_other_deg 1.146 r_chiral_restr 0.098 r_bond_refined_d 0.021 r_gen_planes_refined 0.008 r_bond_other_d 0.005 r_gen_planes_other 0.005 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_mcangle_other r_scbond_other r_scangle_it 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 2950 Nucleic Acid Atoms Solvent Atoms 479 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing