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Truncated S. aureus LytM, P 32 2 1 crystal form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QWY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.5 294 0.1 M Tris, 2.0 M monoammonium dihydrogen phosphate, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 5.26 76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.434 α = 90 b = 100.434 β = 90 c = 103.038 γ = 120
Symmetry Space Group P 32 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 CCD MARRESEARCH 2004-11-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MPG/DESY, HAMBURG BEAMLINE BW6 1.05 MPG/DESY, HAMBURG BW6
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 1.83 20 97.6 0.063 0.063 27.6 3.3 51861 51861 31.9
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) 1.83 1.86 96 0.244 0.244 4.7 2019
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 1QWY 1.83 19.25 49103 49103 2599 97.48 0.18131 0.18131 0.18069 0.2066 0.19313 0.2175 RANDOM 25.468
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] 0.25 0.12 0.25 -0.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.598 r_dihedral_angle_4_deg 29.571 r_dihedral_angle_3_deg 14.679 r_dihedral_angle_1_deg 7.596 r_angle_other_deg 3.997 r_scangle_it 3.645 r_scbond_it 3.149 r_mcangle_it 1.684 r_angle_refined_deg 1.592 r_mcbond_it 1.566
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.598 r_dihedral_angle_4_deg 29.571 r_dihedral_angle_3_deg 14.679 r_dihedral_angle_1_deg 7.596 r_angle_other_deg 3.997 r_scangle_it 3.645 r_scbond_it 3.149 r_mcangle_it 1.684 r_angle_refined_deg 1.592 r_mcbond_it 1.566 r_symmetry_vdw_other 0.252 r_nbd_other 0.23 r_nbd_refined 0.19 r_nbtor_refined 0.18 r_xyhbond_nbd_refined 0.14 r_symmetry_hbond_refined 0.134 r_nbtor_other 0.113 r_symmetry_vdw_refined 0.103 r_chiral_restr 0.1 r_metal_ion_refined 0.055 r_mcbond_other 0.033 r_bond_refined_d 0.014 r_gen_planes_other 0.008 r_gen_planes_refined 0.007 r_bond_other_d r_xyhbond_nbd_other r_metal_ion_other 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 2021 Nucleic Acid Atoms Solvent Atoms 188 Heterogen Atoms 17
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing