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Complex Structure of YejA with fMccA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5ICQ MbnE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 282.15 90 mM BIS-TRIS pH 6.5, 15% (w/v) PEG MME 5000, and 0.5% (w/v) n-dodecyl-beta-D-maltoside
Crystal Properties Matthews coefficient Solvent content 2.43 49.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.523 α = 90 b = 103.121 β = 90 c = 144.01 γ = 90
Symmetry Space Group I 2 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 RAYONIX MX300-HS 2017-07-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 1.78 50 98.3 0.999 41.4 12.4 62999
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.78 1.84 0.917
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.78 83.84 60296 3187 98.34 0.18419 0.18207 0.1927 0.22535 0.2337 RANDOM 29.881
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] 5.8 -2.91 -2.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.121 r_dihedral_angle_4_deg 20.074 r_dihedral_angle_3_deg 15.527 r_long_range_B_refined 6.858 r_long_range_B_other 6.731 r_dihedral_angle_1_deg 6.68 r_scangle_other 5.202 r_scbond_it 3.486 r_scbond_other 3.486 r_mcangle_other 3.141
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.121 r_dihedral_angle_4_deg 20.074 r_dihedral_angle_3_deg 15.527 r_long_range_B_refined 6.858 r_long_range_B_other 6.731 r_dihedral_angle_1_deg 6.68 r_scangle_other 5.202 r_scbond_it 3.486 r_scbond_other 3.486 r_mcangle_other 3.141 r_mcangle_it 3.138 r_mcbond_it 2.259 r_mcbond_other 2.23 r_angle_refined_deg 1.854 r_angle_other_deg 1.095 r_chiral_restr 0.115 r_bond_refined_d 0.018 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.002 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4770 Nucleic Acid Atoms Solvent Atoms 486 Heterogen Atoms
Software Software Software Name Purpose PDB_EXTRACT data extraction autoPROC data processing HKL-2000 data scaling PHENIX phasing