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Crystal structure of the primase-polymerase from Sulfolobus islandicus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RO2 PDB ENTRY 1RO2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 0.1M Tris-HCl pH 8.5, 30-35% PEG 4000, 200mM lithium sulphate, 2mM Tris-2-carboxyethyl-phosphine, VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 2.41 48.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 125.718 α = 90 b = 46.557 β = 124.61 c = 77.993 γ = 90
Symmetry Space Group C 1 2 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 MARRESEARCH M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.93400 ESRF ID14-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.85 50 30362
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 1RO2 1.85 50 28819 1541 94.88 0.20644 0.20408 0.2028 0.25074 0.25 RANDOM 27.222
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] -0.27 0.16 0.7 -0.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.04 r_dihedral_angle_3_deg 18.83 r_dihedral_angle_4_deg 11.957 r_dihedral_angle_1_deg 6.354 r_scangle_it 4.949 r_scbond_it 3.047 r_mcangle_it 1.846 r_angle_refined_deg 1.698 r_mcbond_it 0.968 r_chiral_restr 0.133
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.04 r_dihedral_angle_3_deg 18.83 r_dihedral_angle_4_deg 11.957 r_dihedral_angle_1_deg 6.354 r_scangle_it 4.949 r_scbond_it 3.047 r_mcangle_it 1.846 r_angle_refined_deg 1.698 r_mcbond_it 0.968 r_chiral_restr 0.133 r_bond_refined_d 0.017 r_gen_planes_refined 0.008 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2616 Nucleic Acid Atoms Solvent Atoms 123 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement