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Crystal structure of the F177S mutant of mycrocine immunity protein (MccF) with AMP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GJZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 291 0.2 M potassium chloride, 20% Peg 3350, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.52 51.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 118.23 α = 90 b = 118.23 β = 90 c = 54.839 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315r mirrors 2011-04-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.9794 APS 19-ID
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 2.05 40 98.1 0.083 18 3.9 48175 47231 2 2 47
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.05 2.09 87.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) 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 MOLECULAR REPLACEMENT THROUGHOUT 3GJZ 2.04 40 2 2 47208 44824 2389 97.59 0.18 0.16863 0.16745 0.1755 0.2098 0.2132 RANDOM 39.501
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] -1.34 -1.34 2.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.885 r_dihedral_angle_4_deg 21.845 r_dihedral_angle_3_deg 14.051 r_dihedral_angle_1_deg 6.554 r_angle_refined_deg 1.882 r_angle_other_deg 1.023 r_chiral_restr 0.119 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.885 r_dihedral_angle_4_deg 21.845 r_dihedral_angle_3_deg 14.051 r_dihedral_angle_1_deg 6.554 r_angle_refined_deg 1.882 r_angle_other_deg 1.023 r_chiral_restr 0.119 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 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_mcbond_it r_mcbond_other r_mcangle_it r_scbond_it 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 5278 Nucleic Acid Atoms Solvent Atoms 260 Heterogen Atoms 46
Software Software Software Name Purpose SBC-Collect data collection MOLREP phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling