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Crystal structure of the DNA polymerase III subunit beta from Acinetobacter baumannii
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4K3S
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.6 294 0.1 M Tris-HCl pH 7.6, 0.1 M MgCl2, 7.5%(w/v) PEG 3350, 1% (v/v) DMSO
Crystal Properties Matthews coefficient Solvent content 2.54 51.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.713 α = 90 b = 328.597 β = 91.53 c = 147.497 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 ADSC QUANTUM 315r 2013-09-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.71073 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.95 164.3 99.8 0.115 0.13 0.059 8.4 4.6 144290
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.95 3.06 99.9 0.602 0.681 0.315 0.786 4.6
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 4K3S 2.95 164.3 127602 6719 92.48 0.2503 0.2484 0.2434 0.2867 0.2864 RANDOM 56.624
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] 0.01 0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.514 r_dihedral_angle_3_deg 20.795 r_dihedral_angle_4_deg 20.283 r_dihedral_angle_1_deg 6.935 r_angle_refined_deg 2.522 r_angle_other_deg 1.374 r_chiral_restr 0.192 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 r_bond_other_d 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.514 r_dihedral_angle_3_deg 20.795 r_dihedral_angle_4_deg 20.283 r_dihedral_angle_1_deg 6.935 r_angle_refined_deg 2.522 r_angle_other_deg 1.374 r_chiral_restr 0.192 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 46525 Nucleic Acid Atoms Solvent Atoms 245 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling PHASER phasing HKL-2000 data processing DENZO data reduction