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Crystal structure of Escherichia coli DiaA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2YVA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.9 298 0.1 M Tris pH 8.9, 0.25 M MgCl2, and 32-38% PEG3000
Crystal Properties Matthews coefficient Solvent content 2.1 41.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.49 α = 90 b = 73.82 β = 90 c = 106.37 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 IMAGE PLATE MAR scanner 345 mm plate 2014-04-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
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 1.91 61 100 0.081 13.2 6.9 14941 14941
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 1.91 2 100 0.594 3 6.8
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 2YVA 1.91 60.65 14188 750 99.86 0.1665 0.16489 0.1735 0.19841 0.2065 RANDOM 25.22
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] 4.87 -2.1 -2.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.945 r_dihedral_angle_4_deg 22.24 r_dihedral_angle_3_deg 16.363 r_dihedral_angle_1_deg 6.283 r_long_range_B_other 5.683 r_long_range_B_refined 5.681 r_scangle_other 4.003 r_scbond_it 2.664 r_scbond_other 2.663 r_mcangle_it 2.498
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.945 r_dihedral_angle_4_deg 22.24 r_dihedral_angle_3_deg 16.363 r_dihedral_angle_1_deg 6.283 r_long_range_B_other 5.683 r_long_range_B_refined 5.681 r_scangle_other 4.003 r_scbond_it 2.664 r_scbond_other 2.663 r_mcangle_it 2.498 r_mcangle_other 2.497 r_angle_refined_deg 1.887 r_mcbond_other 1.795 r_mcbond_it 1.794 r_angle_other_deg 0.89 r_chiral_restr 0.104 r_bond_refined_d 0.017 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 1429 Nucleic Acid Atoms Solvent Atoms 48 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement