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Crystal Structure of Pectocin M2 at 1.86 Angstroms
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 1.8 M Ammonium Sulphate, 3% MPD, 0.1 M MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 4.14 70.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.45 α = 90 b = 117.45 β = 90 c = 128.45 γ = 120
Symmetry Space Group P 31 2 1
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 2012-08-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.976 Diamond I02
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 1.86 64.22 100 0.034 47 20 86224 86224 3
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 1.86 1.91 99.8 0.687 5.5 20.8 6313
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 1.86 58.79 81712 81736 4306 99.97 0.1693 0.1693 0.16787 0.1756 0.19714 0.2027 RANDOM 47.237
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] 0.73 0.73 0.73 -2.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.333 r_dihedral_angle_3_deg 14.795 r_dihedral_angle_4_deg 14.257 r_long_range_B_refined 11.094 r_long_range_B_other 11.091 r_scangle_other 7.249 r_dihedral_angle_1_deg 6.713 r_scbond_it 5.731 r_scbond_other 5.731 r_mcangle_it 3.418
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.333 r_dihedral_angle_3_deg 14.795 r_dihedral_angle_4_deg 14.257 r_long_range_B_refined 11.094 r_long_range_B_other 11.091 r_scangle_other 7.249 r_dihedral_angle_1_deg 6.713 r_scbond_it 5.731 r_scbond_other 5.731 r_mcangle_it 3.418 r_mcangle_other 3.418 r_mcbond_it 2.7 r_mcbond_other 2.686 r_angle_refined_deg 2.546 r_angle_other_deg 1.021 r_chiral_restr 0.143 r_bond_refined_d 0.024 r_gen_planes_refined 0.012 r_bond_other_d 0.002 r_gen_planes_other 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4113 Nucleic Acid Atoms Solvent Atoms 438 Heterogen Atoms 389
Software Software Software Name Purpose xia2 data scaling PHENIX model building REFMAC refinement XDS data reduction XDS data scaling PHENIX phasing