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Crystal structure of DpaA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4XZZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 295 19-25% (w/v) PEG 3350, 0.1M Bis-Tris-HCl, pH 6-7, 0.2M ammonium acetate
Crystal Properties Matthews coefficient Solvent content 2.62 52.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.876 α = 90 b = 86.876 β = 90 c = 150.675 γ = 90
Symmetry Space Group P 4 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 80 CCD RAYONIX MX300HE 2020-07-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL15A1 1 NSRRC BL15A1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim I (All) 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 2.9 28.47 99.5 0.019 0.999 26.07 2 13361
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.9 3.004 0.2015 0.982
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.9 28.47 12702 661 99.49 0.21747 0.21461 0.2737 0.2613 RANDOM 111.576
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] 0.09 0.09 -0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 19.113 r_dihedral_angle_2_deg 12.439 r_dihedral_angle_1_deg 9.5 r_long_range_B_refined 7.394 r_long_range_B_other 7.394 r_scangle_other 4.867 r_mcangle_it 4.752 r_mcangle_other 4.751 r_scbond_it 3.105 r_scbond_other 3.104
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 19.113 r_dihedral_angle_2_deg 12.439 r_dihedral_angle_1_deg 9.5 r_long_range_B_refined 7.394 r_long_range_B_other 7.394 r_scangle_other 4.867 r_mcangle_it 4.752 r_mcangle_other 4.751 r_scbond_it 3.105 r_scbond_other 3.104 r_mcbond_it 2.936 r_mcbond_other 2.936 r_angle_refined_deg 1.855 r_rigid_bond_restr 1.717 r_angle_other_deg 0.785 r_chiral_restr 0.079 r_bond_refined_d 0.01 r_gen_planes_other 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_dihedral_angle_4_deg 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3033 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHENIX phasing