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Protein-folding location can regulate Mn versus Cu- or Zn-binding. Crystal Structure of MncA.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1L3J PDB ENTRY 1L3J
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4.2 0.1M SODIUM ACETATE PH 3.25, 8% W/V PEG8000
Crystal Properties Matthews coefficient Solvent content 4.2 70.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 236.19 α = 90 b = 236.19 β = 90 c = 134.041 γ = 120
Symmetry Space Group P 65 2 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 MARRESEARCH M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 ESRF BM14
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 2.95 68.2 100 0.18 13.4 10.9 46724
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 2.95 3.11 100 0.43 5.6 11.2
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 1L3J 2.95 58.32 44297 2386 100 0.193 0.191 0.1932 0.233 0.2295 RANDOM 12.42
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] -0.34 -0.17 -0.34 0.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.819 r_dihedral_angle_4_deg 19.519 r_dihedral_angle_3_deg 16.215 r_dihedral_angle_1_deg 6.067 r_angle_refined_deg 1.308 r_nbtor_refined 0.331 r_symmetry_vdw_refined 0.261 r_symmetry_hbond_refined 0.253 r_nbd_refined 0.232 r_xyhbond_nbd_refined 0.155
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.819 r_dihedral_angle_4_deg 19.519 r_dihedral_angle_3_deg 16.215 r_dihedral_angle_1_deg 6.067 r_angle_refined_deg 1.308 r_nbtor_refined 0.331 r_symmetry_vdw_refined 0.261 r_symmetry_hbond_refined 0.253 r_nbd_refined 0.232 r_xyhbond_nbd_refined 0.155 r_chiral_restr 0.081 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8236 Nucleic Acid Atoms Solvent Atoms 32 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling AMoRE phasing