☰ Navigation Tabs
Phi29 DNA polymerase complexed with single-stranded DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XHX copy C of 1XHX without residues 359-394
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 0.1 M MES pH 6.5, 12% PEG 20,000, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal Properties Matthews coefficient Solvent content 2.37 48.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.195 α = 90 b = 200.178 β = 109.4 c = 66.989 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 315 2006-08-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C APS 24-ID-C
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 1.601 50 97.8 0.045 49.9 6.9 176187 172311 -3
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) 1.601 1.66 92.2 0.44 3.7 5.5
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT copy C of 1XHX without residues 359-394 1.6 40.59 176187 163498 8614 97.83 0.16547 0.16399 0.19363 0.2588 RANDOM 26.563
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] -0.23 -0.16 -0.12 0.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.81 r_dihedral_angle_3_deg 12.333 r_dihedral_angle_4_deg 12.06 r_dihedral_angle_1_deg 6.049 r_scangle_it 3.044 r_mcangle_it 2.333 r_scbond_it 2.108 r_mcbond_it 1.689 r_angle_refined_deg 1.201 r_angle_other_deg 0.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.81 r_dihedral_angle_3_deg 12.333 r_dihedral_angle_4_deg 12.06 r_dihedral_angle_1_deg 6.049 r_scangle_it 3.044 r_mcangle_it 2.333 r_scbond_it 2.108 r_mcbond_it 1.689 r_angle_refined_deg 1.201 r_angle_other_deg 0.8 r_mcbond_other 0.486 r_symmetry_hbond_refined 0.244 r_nbd_refined 0.202 r_nbtor_refined 0.187 r_nbd_other 0.186 r_symmetry_vdw_other 0.174 r_symmetry_vdw_refined 0.168 r_xyhbond_nbd_refined 0.129 r_nbtor_other 0.084 r_chiral_restr 0.072 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9267 Nucleic Acid Atoms 532 Solvent Atoms 1493 Heterogen Atoms 108
Software Software Software Name Purpose ADSC data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling