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Crystal structure of reduced DsbA3 from Neisseria meningitidis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3DVW PDB ENTRY 3DVW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 2.2 M Ammonium sulfate, 0.25 M Sodium malonate, 0.1 M MES pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 281K
Crystal Properties Matthews coefficient Solvent content 2.77 55.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 159.979 α = 90 b = 159.979 β = 90 c = 76.888 γ = 90
Symmetry Space Group I 41 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 ADSC QUANTUM 4 TOROIDAL MIRROR M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-3 ESRF ID14-3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.8 20 100 0.099 6.3 12.9 12602 61
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.8 2.95 100 0.272 2.7 13.2
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 PDB ENTRY 3DVW 2.8 19.79 11936 610 100 0.22964 0.22669 0.2304 0.28605 0.2914 RANDOM 31.545
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] -0.15 -0.15 0.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.839 r_dihedral_angle_4_deg 21.509 r_dihedral_angle_3_deg 20.783 r_dihedral_angle_1_deg 5.946 r_angle_refined_deg 1.177 r_mcangle_it 1.034 r_angle_other_deg 0.739 r_scangle_it 0.643 r_mcbond_it 0.601 r_scbond_it 0.424
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.839 r_dihedral_angle_4_deg 21.509 r_dihedral_angle_3_deg 20.783 r_dihedral_angle_1_deg 5.946 r_angle_refined_deg 1.177 r_mcangle_it 1.034 r_angle_other_deg 0.739 r_scangle_it 0.643 r_mcbond_it 0.601 r_scbond_it 0.424 r_nbd_refined 0.25 r_symmetry_vdw_other 0.244 r_xyhbond_nbd_refined 0.224 r_nbd_other 0.223 r_symmetry_vdw_refined 0.218 r_nbtor_refined 0.2 r_symmetry_hbond_refined 0.18 r_xyhbond_nbd_other 0.116 r_nbtor_other 0.095 r_mcbond_other 0.079 r_chiral_restr 0.063 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2952 Nucleic Acid Atoms Solvent Atoms 23 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing