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The Crystal Structure of Pectocin M2 at 2.3 Angstroms
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4N58 pdb entry 4N58
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 15 % PEG3350, 0.2 M Ammonium sulphate, 3% MPD, 0.1M Bis-tris, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.55 51.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.649 α = 90 b = 116.745 β = 94.96 c = 60.79 γ = 90
Symmetry Space Group P 1 21 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 2012-09-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.0 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 2.3 50 96.6 0.05 12.41 3.2 55667 52652 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 2.3 2.44 95.7 0.599 1.85 2.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 SAD THROUGHOUT pdb entry 4N58 2.3 44.52 26250 26116 1384 99.49 0.20964 0.20634 0.2011 0.27369 0.2644 RANDOM 67.992
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] -0.08 -0.59 -1.4 1.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.071 r_dihedral_angle_3_deg 17.141 r_dihedral_angle_4_deg 13.398 r_long_range_B_refined 8.263 r_long_range_B_other 8.254 r_dihedral_angle_1_deg 6.752 r_scangle_other 4.687 r_mcangle_other 4.374 r_mcangle_it 4.12 r_scbond_it 3.053
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.071 r_dihedral_angle_3_deg 17.141 r_dihedral_angle_4_deg 13.398 r_long_range_B_refined 8.263 r_long_range_B_other 8.254 r_dihedral_angle_1_deg 6.752 r_scangle_other 4.687 r_mcangle_other 4.374 r_mcangle_it 4.12 r_scbond_it 3.053 r_scbond_other 2.944 r_mcbond_it 2.461 r_mcbond_other 2.457 r_angle_refined_deg 1.7 r_angle_other_deg 0.866 r_chiral_restr 0.101 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_bond_other_d 0.001 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 4079 Nucleic Acid Atoms Solvent Atoms 51 Heterogen Atoms 34
Software Software Software Name Purpose XDS data scaling PHASER phasing REFMAC refinement XDS data reduction