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The crystal structure of MnmC from Yersinia pestis bound with FAD and SAM
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3PVC pdb entry 3PVC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 310 0.1M HEPES PH 7.0
30% (v/v) Jeffamine ED-2001 PH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 100K, temperature 310K
Crystal Properties Matthews coefficient Solvent content 2.53 51.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.085 α = 90 b = 59.815 β = 100.18 c = 100.797 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 CCD ADSC QUANTUM 315r 2010-11-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 0.9790 NSLS X29A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.7 50 100 0.143 0.177 9.3 5.1 21571 21571
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.75 100 0.734 0.819 2.1 5.2
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 3PVC 2.7 50 18983 1022 92.68 0.18413 0.1801 0.1773 0.25933 0.2506 RANDOM 25.751
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] -0.2 -0.3 0.51 -0.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.37 r_dihedral_angle_3_deg 18.607 r_dihedral_angle_4_deg 18.183 r_dihedral_angle_1_deg 5.746 r_scangle_it 4.774 r_scbond_it 2.942 r_mcangle_it 1.712 r_angle_refined_deg 1.491 r_mcbond_it 0.868 r_chiral_restr 0.093
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.37 r_dihedral_angle_3_deg 18.607 r_dihedral_angle_4_deg 18.183 r_dihedral_angle_1_deg 5.746 r_scangle_it 4.774 r_scbond_it 2.942 r_mcangle_it 1.712 r_angle_refined_deg 1.491 r_mcbond_it 0.868 r_chiral_restr 0.093 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4916 Nucleic Acid Atoms Solvent Atoms 91 Heterogen Atoms 81
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling