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Crystal structure of pneumococcal surface antigen PsaA in the Cd- bound, closed state
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PSZ PDB ENTRY 1PSZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8 26-36 % PEG 400, 0.1 M NACL, 0.1 M TRIZMA-HCL PH 8.0 AND 0.1 M CDCL2
Crystal Properties Matthews coefficient Solvent content 2.37 48.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.239 α = 90 b = 47.911 β = 106.96 c = 101.524 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 193 CCD ADSC CCD M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 Australian Synchrotron MX2
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 43 93.8 0.11 5.24 1.9 36157 2
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 2.07 93.9 0.67 3.13 1.9
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 1PSZ 2 42.97 34346 1814 93.78 0.22249 0.22052 0.1927 0.26028 0.2285 RANDOM 39.319
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] 20.12 -14.71 -16.33 -3.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.494 r_dihedral_angle_4_deg 17.812 r_dihedral_angle_3_deg 14.247 r_dihedral_angle_1_deg 5.213 r_mcangle_it 2.104 r_scbond_it 1.556 r_mcbond_it 1.267 r_angle_refined_deg 0.969 r_chiral_restr 0.072 r_bond_refined_d 0.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.494 r_dihedral_angle_4_deg 17.812 r_dihedral_angle_3_deg 14.247 r_dihedral_angle_1_deg 5.213 r_mcangle_it 2.104 r_scbond_it 1.556 r_mcbond_it 1.267 r_angle_refined_deg 0.969 r_chiral_restr 0.072 r_bond_refined_d 0.005 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4518 Nucleic Acid Atoms Solvent Atoms 124 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement REFMAC phasing