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LytM domain of DipM, a coordinator of a complex net of autolysins in Caulobacter crescentus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5KVP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 291 0.02M Magnesium chloride, 0.1M Hepes pH 7.5 and 22% Polyacrylic acid sodium salt 5100 .
Crystal Properties Matthews coefficient Solvent content 2.8 56.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.869 α = 90 b = 105.839 β = 90 c = 108.431 γ = 90
Symmetry Space Group P 2 21 21
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 2020-07-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.979185 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.25 49.75 100 0.102 0.99 8 11.1 36758
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.25 2.32 100 0.474 0.703 2.1 11.1
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5KVP 2.25 49.75 34958 1754 99.98 0.1892 0.1877 0.191 0.2191 0.2273 RANDOM 25.599
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] -1.38 1.54 -0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.65 r_dihedral_angle_4_deg 23.015 r_dihedral_angle_3_deg 15.511 r_dihedral_angle_1_deg 7.306 r_angle_refined_deg 1.569 r_angle_other_deg 1.304 r_chiral_restr 0.07 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.65 r_dihedral_angle_4_deg 23.015 r_dihedral_angle_3_deg 15.511 r_dihedral_angle_1_deg 7.306 r_angle_refined_deg 1.569 r_angle_other_deg 1.304 r_chiral_restr 0.07 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4352 Nucleic Acid Atoms Solvent Atoms 471 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling PHASER phasing