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Crystal structure of the catalytic domain of primase Repb' in complex with initiator DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3H20 CATALYTIC DOMAIN OF PDB 3H20, MODEL OF IDEAL B-DNA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5 0.2M AMMONIUM CITRATE, 20% PEG 3350, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K
Crystal Properties Matthews coefficient Solvent content 1.88 34.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.35 α = 90 b = 85.35 β = 90 c = 68.89 γ = 90
Symmetry Space Group P 43 21 2
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 MAR CCD 165 mm MIRRORS 2007-12-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.91841 BESSY 14.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.7 19 97.5 0.111 16.51 7.2 7400 7215 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.77 95 0.394 5.64 7.3
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 CATALYTIC DOMAIN OF PDB 3H20, MODEL OF IDEAL B-DNA 2.7 19 6997 368 100 0.226 0.224 0.2291 0.274 0.2764 RANDOM 31.47
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 0.36 -0.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.977 r_dihedral_angle_4_deg 15.321 r_dihedral_angle_3_deg 15.163 r_dihedral_angle_1_deg 4.605 r_angle_refined_deg 0.947 r_scangle_it 0.658 r_mcangle_it 0.353 r_scbond_it 0.333 r_nbtor_refined 0.28 r_mcbond_it 0.198
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.977 r_dihedral_angle_4_deg 15.321 r_dihedral_angle_3_deg 15.163 r_dihedral_angle_1_deg 4.605 r_angle_refined_deg 0.947 r_scangle_it 0.658 r_mcangle_it 0.353 r_scbond_it 0.333 r_nbtor_refined 0.28 r_mcbond_it 0.198 r_nbd_refined 0.158 r_symmetry_vdw_refined 0.125 r_xyhbond_nbd_refined 0.106 r_symmetry_hbond_refined 0.068 r_chiral_restr 0.051 r_bond_refined_d 0.005 r_gen_planes_refined 0.002 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_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 1417 Nucleic Acid Atoms 546 Solvent Atoms 24 Heterogen Atoms
Software Software Software Name Purpose PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling