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Truncated S. aureus LytM, P41 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 6.5 294 30 % PEG 8000, 0.2 M L(+)-tartrate, 0.1 M MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.34 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.962 α = 90 b = 65.962 β = 90 c = 62.96 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MARRESEARCH Osmic Max-Flux 2005-03-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300
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 1.55 14.8 96.3 0.037 0.037 25.8 2.2 38546 38546 15
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 1.55 1.58 86.1 0.152 0.152 10 1803
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 1.55 14.8 36606 36606 1940 98.2 0.17303 0.17303 0.17157 0.176 0.20054 0.1987 RANDOM 12.214
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] -0.19 -0.19 0.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.79 r_angle_other_deg 3.994 r_scangle_it 3.779 r_scbond_it 2.417 r_mcangle_it 1.511 r_angle_refined_deg 1.48 r_mcbond_it 0.87 r_nbd_other 0.298 r_symmetry_vdw_other 0.289 r_nbd_refined 0.222
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.79 r_angle_other_deg 3.994 r_scangle_it 3.779 r_scbond_it 2.417 r_mcangle_it 1.511 r_angle_refined_deg 1.48 r_mcbond_it 0.87 r_nbd_other 0.298 r_symmetry_vdw_other 0.289 r_nbd_refined 0.222 r_xyhbond_nbd_refined 0.141 r_symmetry_hbond_refined 0.136 r_nbtor_other 0.115 r_symmetry_vdw_refined 0.107 r_chiral_restr 0.096 r_metal_ion_refined 0.036 r_bond_refined_d 0.013 r_gen_planes_other 0.009 r_gen_planes_refined 0.007 r_bond_other_d r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_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 2004 Nucleic Acid Atoms Solvent Atoms 342 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing