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Crystal structure of E. coli MccB + AMPCPP + SeMeT MccA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3H9G PDB entry 3H9G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 291.2 24-26% Pentaerythritol ethoxylate (15/4 EO/OH, Hampton Research), 50 mM Na Hepes pH 7.5, 100 mM MgSO4, 9 mM AMPCPP, VAPOR DIFFUSION, HANGING DROP, temperature 291.2K
Crystal Properties Matthews coefficient Solvent content 1.93 36.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.841 α = 90 b = 138.004 β = 92.21 c = 80.816 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 IMAGE PLATE MAR scanner 300 mm plate Rosenbaum-Rock vertical focusing mirror 2007-12-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 0.97926 APS 22-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 2.3 50 98.9 0.081 17.14 4.1 54611 54611 41.7
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 2.38 91.1 0.364 3.3 5027
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 (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 FOURIER SYNTHESIS THROUGHOUT PDB entry 3H9G 2.3 39.97 54215 53753 2715 99.16 0.203 0.199 0.196 0.2261 0.255 0.2776 RANDOM 44.194
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] 0.73 -0.08 -1.57 0.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.605 r_dihedral_angle_4_deg 19.488 r_dihedral_angle_3_deg 16.999 r_dihedral_angle_1_deg 5.873 r_scangle_it 1.972 r_angle_refined_deg 1.248 r_scbond_it 1.229 r_mcangle_it 0.912 r_mcbond_it 0.511 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.605 r_dihedral_angle_4_deg 19.488 r_dihedral_angle_3_deg 16.999 r_dihedral_angle_1_deg 5.873 r_scangle_it 1.972 r_angle_refined_deg 1.248 r_scbond_it 1.229 r_mcangle_it 0.912 r_mcbond_it 0.511 r_nbtor_refined 0.303 r_symmetry_vdw_refined 0.205 r_nbd_refined 0.198 r_xyhbond_nbd_refined 0.162 r_symmetry_hbond_refined 0.141 r_chiral_restr 0.083 r_bond_refined_d 0.01 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10482 Nucleic Acid Atoms Solvent Atoms 223 Heterogen Atoms 142
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction X-GEN data scaling HKL-2000 data reduction REFMAC phasing