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Structure of the P176A 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 2.9 57.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.832 α = 90 b = 114.772 β = 90 c = 225.402 γ = 90
Symmetry Space Group C 2 2 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 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 2.14 47 99 0.19 9.2 6.3 36063 2
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 2.14 2.19 94.2 0.82 2 4.9
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 2.14 46.94 36063 1898 100 0.19069 0.18804 0.1907 0.24104 0.2428 RANDOM 26.938
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] -0.02 0.05 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.137 r_dihedral_angle_4_deg 16.206 r_dihedral_angle_3_deg 15.353 r_dihedral_angle_1_deg 6.52 r_scangle_it 5.261 r_scbond_it 3.398 r_angle_refined_deg 2.027 r_mcangle_it 1.929 r_mcbond_it 1.069 r_chiral_restr 0.131
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.137 r_dihedral_angle_4_deg 16.206 r_dihedral_angle_3_deg 15.353 r_dihedral_angle_1_deg 6.52 r_scangle_it 5.261 r_scbond_it 3.398 r_angle_refined_deg 2.027 r_mcangle_it 1.929 r_mcbond_it 1.069 r_chiral_restr 0.131 r_bond_refined_d 0.023 r_gen_planes_refined 0.011 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 4134 Nucleic Acid Atoms Solvent Atoms 232 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing