☰ Navigation Tabs
Crystal structure of DNA polymerase III, beta chain (EC 2.7.7.7) (np_344555.1) from STREPTOCOCCUS PNEUMONIAE TIGR4 at 2.50 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MMI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION,SITTING DROP,NANODROP 7.5 277 10.0% iso-Propanol, 20.0% PEG-4000, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.76 55.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.06 α = 90 b = 70.72 β = 91.04 c = 135.44 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 100 CCD MARMOSAIC 325 mm CCD 2005-06-02 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.97934, 0.91837, 0.97923 SSRL BL9-2
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 2.5 48.9 91.1 0.088 8 59570
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 2.5 2.6 74.4 0.678 1.85
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD, MOLECULAR REPLACEMENT THROUGHOUT 1MMI 2.5 30 56494 3044 48.91 0.195 0.192 0.1965 0.25 0.2509 RANDOM 60.175
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] -0.36 -2.72 -2.04 2.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.874 r_dihedral_angle_4_deg 16.323 r_dihedral_angle_3_deg 15.183 r_scangle_it 7.047 r_dihedral_angle_1_deg 6.467 r_scbond_it 4.657 r_mcangle_it 2.551 r_mcbond_it 1.542 r_angle_refined_deg 1.294 r_angle_other_deg 0.735
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.874 r_dihedral_angle_4_deg 16.323 r_dihedral_angle_3_deg 15.183 r_scangle_it 7.047 r_dihedral_angle_1_deg 6.467 r_scbond_it 4.657 r_mcangle_it 2.551 r_mcbond_it 1.542 r_angle_refined_deg 1.294 r_angle_other_deg 0.735 r_mcbond_other 0.291 r_symmetry_vdw_other 0.206 r_nbd_refined 0.202 r_nbtor_refined 0.174 r_nbd_other 0.173 r_xyhbond_nbd_refined 0.146 r_nbtor_other 0.083 r_chiral_restr 0.073 r_symmetry_hbond_refined 0.073 r_symmetry_vdw_refined 0.071 r_bond_refined_d 0.012 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11381 Nucleic Acid Atoms Solvent Atoms 251 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction SHELXD phasing autoSHARP phasing MOLREP phasing