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Crystal structure of E. coli MccB + MccA-N7isoASN
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3H5A PDB entry 3H5A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 291.2 24-26% Pentaerythritol ethoxylate (15/4 EO/OH, Hampton Research), 50 mM Tris-HCl pH 8.0, 50 mM (NH4)2SO4, 10 mM MccA-N7isoAsn, VAPOR DIFFUSION, HANGING DROP, temperature 291.2K
Crystal Properties Matthews coefficient Solvent content 1.94 36.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.929 α = 90 b = 138.217 β = 92.38 c = 80.799 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 2.2 50 96.7 0.065 21.914 4.1 60798 60798 33.6
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 2.2 2.28 90.5 0.371 3.6 5645
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 MOLECULAR REPLACEMENT THROUGHOUT PDB entry 3H5A 2.2 46.88 62124 60091 3041 96.73 0.206 0.203 0.203 0.2021 0.261 0.2583 RANDOM 36.297
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] 0.44 -0.03 -1.05 0.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.142 r_dihedral_angle_4_deg 17.641 r_dihedral_angle_3_deg 15.297 r_dihedral_angle_1_deg 5.28 r_scangle_it 2.217 r_scbond_it 1.591 r_mcangle_it 1.116 r_angle_refined_deg 1.103 r_mcbond_it 0.794 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.142 r_dihedral_angle_4_deg 17.641 r_dihedral_angle_3_deg 15.297 r_dihedral_angle_1_deg 5.28 r_scangle_it 2.217 r_scbond_it 1.591 r_mcangle_it 1.116 r_angle_refined_deg 1.103 r_mcbond_it 0.794 r_nbtor_refined 0.303 r_nbd_refined 0.201 r_symmetry_vdw_refined 0.195 r_xyhbond_nbd_refined 0.146 r_symmetry_hbond_refined 0.131 r_chiral_restr 0.075 r_bond_refined_d 0.009 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10767 Nucleic Acid Atoms Solvent Atoms 511 Heterogen Atoms 39
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 PHASER phasing