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The crystal structure of the Lactococcus lactis MG1363 DpsA protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZS3 PDB entry 1ZS3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 1.7M ammonium sulphate, 0.1M HEPES/Na, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.26 58.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 131.84 α = 90 b = 131.84 β = 90 c = 325.7 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 298 CCD ADSC QUANTUM 4 Mirrors 2001-12-05 M SINGLE WAVELENGTH 2 1 x-ray 298 CCD ADSC QUANTUM 4 Mirrors 2001-12-05 M SINGLE WAVELENGTH 1,2 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX14.1 1.488 SRS PX14.1 2 SYNCHROTRON SRS BEAMLINE PX14.1 1.488 SRS PX14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.9 15 94.5 0.078 0.078 6.7 2.6 22949 22949 77.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1,2 2.9 3.06 93.8 0.382 0.382 1.7 2.6 3298
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1ZS3 2.9 15 20210 20210 1098 87.06 0.25622 0.25622 0.25256 0.32216 RANDOM 53.953
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] 1.35 0.67 1.35 -2.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 10.114 r_scangle_it 2.173 r_angle_refined_deg 1.566 r_scbond_it 1.224 r_mcangle_it 0.973 r_angle_other_deg 0.933 r_mcbond_it 0.504 r_symmetry_vdw_refined 0.277 r_nbd_refined 0.253 r_nbd_other 0.231
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 10.114 r_scangle_it 2.173 r_angle_refined_deg 1.566 r_scbond_it 1.224 r_mcangle_it 0.973 r_angle_other_deg 0.933 r_mcbond_it 0.504 r_symmetry_vdw_refined 0.277 r_nbd_refined 0.253 r_nbd_other 0.231 r_symmetry_vdw_other 0.211 r_xyhbond_nbd_refined 0.18 r_chiral_restr 0.096 r_nbtor_other 0.093 r_symmetry_hbond_refined 0.021 r_bond_refined_d 0.014 r_gen_planes_refined 0.005 r_gen_planes_other 0.003 r_bond_other_d 0.002 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5544 Nucleic Acid Atoms Solvent Atoms 45 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling TNT phasing