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DNA Polymerase PolC from Geobacillus kaustophilus complex with DNA, dGTP, Mn and Zn
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3F2B PDB entry 3F2B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.3 289 20% PEG 2000 MME, 0.1M PHOSPHATE CITRATE, 200MM LITHIUM SULFATE, 1 mM ZnCl2, 2 mM MnCl2, pH 5.30, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.87 57.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 115.997 α = 90 b = 139.479 β = 90 c = 184.074 γ = 90
Symmetry Space Group C 2 2 21
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 2008-04-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.999887 ALS 5.0.1
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 43.15 99.8 0.087 11.2 4.9 50821
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 2.59 99 0.642 4.2
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 3F2B 2.51 43.15 50750 2573 0.218 0.216 0.2145 0.254 0.2508 RANDOM 46.38
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] -2.16 1.01 1.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.525 r_dihedral_angle_3_deg 20.591 r_dihedral_angle_4_deg 18.887 r_dihedral_angle_1_deg 5.964 r_scangle_it 2.479 r_angle_refined_deg 1.701 r_scbond_it 1.547 r_mcangle_it 0.934 r_mcbond_it 0.48 r_chiral_restr 0.101
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.525 r_dihedral_angle_3_deg 20.591 r_dihedral_angle_4_deg 18.887 r_dihedral_angle_1_deg 5.964 r_scangle_it 2.479 r_angle_refined_deg 1.701 r_scbond_it 1.547 r_mcangle_it 0.934 r_mcbond_it 0.48 r_chiral_restr 0.101 r_bond_refined_d 0.013 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 7796 Nucleic Acid Atoms 631 Solvent Atoms 101 Heterogen Atoms 46
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling