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Crystal structure of the S111A mutant of member of MccF clade from Listeria monocytogenes EGD-e with product
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4H1H
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 289 35%MPD, imidazole, 0.1 MgCl2, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 3.03 59.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.242 α = 90 b = 92.242 β = 90 c = 205.776 γ = 90
Symmetry Space Group P 41 21 2
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 2012-12-12 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 2.4 40 97.3 0.9 17 3.2 35790 34854 2 2 56
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 2.4 2.44 99
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4H1H 2.4 38.32 2 2 34834 33087 1747 97.37 0.19281 0.19017 0.2429 0.2227 RANDOM 45.794
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] 1.62 1.62 -3.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.949 r_dihedral_angle_4_deg 18.534 r_dihedral_angle_3_deg 16.591 r_dihedral_angle_1_deg 7.064 r_angle_refined_deg 1.678 r_angle_other_deg 0.822 r_chiral_restr 0.09 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.949 r_dihedral_angle_4_deg 18.534 r_dihedral_angle_3_deg 16.591 r_dihedral_angle_1_deg 7.064 r_angle_refined_deg 1.678 r_angle_other_deg 0.822 r_chiral_restr 0.09 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 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_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 5000 Nucleic Acid Atoms Solvent Atoms 175 Heterogen Atoms 84
Software Software Software Name Purpose SBC-Collect data collection MOLREP phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling