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Crystal structure of Enterobacteria phage RB69 gp43 DNA polymerase complexed with tetrahydrofuran containing DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1CLQ PDB ENTRY 1CLQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 298 PEG 350MME, Calcium chloride, Tris-HCl, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 6.50
Crystal Properties Matthews coefficient Solvent content 2.89 57.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 131.948 α = 90 b = 122.237 β = 96.85 c = 165.358 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 4 2002-09-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X26C NSLS X26C
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 2.69 47 94.7 0.113 19.1 4.8 137338
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 2.69 2.8 73.3 0.434 1.8
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 (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 1CLQ 2.69 47 142376 130465 6841 94.7 0.21879 0.21512 0.2078 0.2879 0.2734 RANDOM 22.067
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] -2.45 0.02 2.28 0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.509 r_scangle_it 2.295 r_angle_refined_deg 1.535 r_scbond_it 1.456 r_mcangle_it 0.819 r_mcbond_it 0.417 r_metal_ion_refined 0.233 r_nbd_refined 0.229 r_symmetry_vdw_refined 0.229 r_symmetry_hbond_refined 0.212
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.509 r_scangle_it 2.295 r_angle_refined_deg 1.535 r_scbond_it 1.456 r_mcangle_it 0.819 r_mcbond_it 0.417 r_metal_ion_refined 0.233 r_nbd_refined 0.229 r_symmetry_vdw_refined 0.229 r_symmetry_hbond_refined 0.212 r_xyhbond_nbd_refined 0.189 r_chiral_restr 0.106 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_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 29460 Nucleic Acid Atoms 2532 Solvent Atoms 535 Heterogen Atoms 229
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing