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Crystal structure of the receiver domain of LytR from Staphylococcus aureus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QVO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277 100 mM MES (pH 6.5), 1.6 M magnesium sulfate heptahydrate
Crystal Properties Matthews coefficient Solvent content 5.44 77.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.747 α = 90 b = 84.747 β = 90 c = 157.304 γ = 120
Symmetry Space Group P 61 2 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 RAYONIX MX-300 2013-08-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.9795 CLSI 08ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.5 42.66 99.9 0.087 0.089 0.026 0.998 20.3 20.9 12211 80.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.6 99.7 2.607 2.669 0.781 0.91 1.8 21.5
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2qvo 2.5 42.7 11533 628 99.87 0.20136 0.19944 0.23666 0.2467 RANDOM 91.566
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] 2.05 1.03 2.05 -6.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.986 r_dihedral_angle_3_deg 18.895 r_dihedral_angle_4_deg 15.048 r_long_range_B_other 9.107 r_long_range_B_refined 9.102 r_scangle_other 8.386 r_dihedral_angle_1_deg 7.466 r_mcangle_it 7.396 r_mcangle_other 7.392 r_scbond_it 6.407
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.986 r_dihedral_angle_3_deg 18.895 r_dihedral_angle_4_deg 15.048 r_long_range_B_other 9.107 r_long_range_B_refined 9.102 r_scangle_other 8.386 r_dihedral_angle_1_deg 7.466 r_mcangle_it 7.396 r_mcangle_other 7.392 r_scbond_it 6.407 r_scbond_other 5.971 r_mcbond_it 5.39 r_mcbond_other 5.253 r_angle_refined_deg 2.306 r_angle_other_deg 1.278 r_chiral_restr 0.113 r_bond_refined_d 0.022 r_gen_planes_refined 0.011 r_gen_planes_other 0.002 r_bond_other_d 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 930 Nucleic Acid Atoms Solvent Atoms 13 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASES phasing