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LytR LCP domain from Streptococcus dysgalactiae subs. dysgalactiae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3OKZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 292 2.2 M ammonium sulphate
20% glycerol
Crystal Properties Matthews coefficient Solvent content 4.96 75.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 141.271 α = 90 b = 141.271 β = 90 c = 133.742 γ = 90
Symmetry Space Group I 4 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 PIXEL DECTRIS PILATUS 6M 2016-07-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.966 ESRF MASSIF-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.8 48.608 99.9 0.999 15.5 8 16955
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.95 0.666
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.8 48.608 16955 895 99.776 0.272 0.2714 0.2719 0.2927 0.2917 80.154
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] -0.932 -0.932 1.865
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 24.182 r_dihedral_angle_2_deg 18.605 r_dihedral_angle_6_deg 16.352 r_lrange_it 6.437 r_lrange_other 6.437 r_dihedral_angle_1_deg 6.143 r_mcangle_it 5.689 r_mcangle_other 5.687 r_scangle_other 4.5 r_scangle_it 4.475
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 24.182 r_dihedral_angle_2_deg 18.605 r_dihedral_angle_6_deg 16.352 r_lrange_it 6.437 r_lrange_other 6.437 r_dihedral_angle_1_deg 6.143 r_mcangle_it 5.689 r_mcangle_other 5.687 r_scangle_other 4.5 r_scangle_it 4.475 r_mcbond_it 4.044 r_mcbond_other 4.044 r_scbond_other 2.678 r_scbond_it 2.661 r_angle_refined_deg 1.968 r_symmetry_nbd_refined 0.722 r_symmetry_xyhbond_nbd_refined 0.691 r_angle_other_deg 0.623 r_nbd_other 0.517 r_nbd_refined 0.249 r_symmetry_nbd_other 0.225 r_nbtor_refined 0.181 r_xyhbond_nbd_refined 0.133 r_chiral_restr 0.089 r_symmetry_nbtor_other 0.084 r_bond_refined_d 0.017 r_gen_planes_refined 0.008 r_gen_planes_other 0.002 r_bond_other_d 0.001 r_ext_dist_refined_b
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2076 Nucleic Acid Atoms Solvent Atoms 25 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MrBUMP phasing