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Structure of the P107A Colicin M mutant from E. coli
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2XMX PDB ENTRY 2XMX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 20% PEG3350 0.2 M NANO3, pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.42 48.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.852 α = 87.59 b = 63.114 β = 82.17 c = 189.34 γ = 65.65
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 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.31 49 89.5 0.09 5.4 1.7 85754 1.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.31 2.37 72.9 0.4 1.5 1.5
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2XMX 2.31 48.68 85754 4514 100 0.24185 0.24023 0.2421 0.27261 0.2766 RANDOM 21.646
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] -0.05 0.17 -0.11 -0.5 0.01 0.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.586 r_dihedral_angle_4_deg 19.466 r_dihedral_angle_3_deg 14.932 r_dihedral_angle_1_deg 6.021 r_scangle_it 4.845 r_scbond_it 2.785 r_mcangle_it 1.584 r_angle_refined_deg 1.43 r_mcbond_it 0.784 r_chiral_restr 0.099
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.586 r_dihedral_angle_4_deg 19.466 r_dihedral_angle_3_deg 14.932 r_dihedral_angle_1_deg 6.021 r_scangle_it 4.845 r_scbond_it 2.785 r_mcangle_it 1.584 r_angle_refined_deg 1.43 r_mcbond_it 0.784 r_chiral_restr 0.099 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16536 Nucleic Acid Atoms Solvent Atoms 451 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing