☰ Navigation Tabs
Crystal structure of DNA polymerase lambda complexed with a two nucleotide gap DNA molecule
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BPY polymerase beta
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 279 cacodylate, sodium acetate, PEG8000, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 279K
Crystal Properties Matthews coefficient Solvent content 2.86 56.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 191.321 α = 90 b = 99.034 β = 90 c = 104.838 γ = 90
Symmetry Space Group P 21 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 93 IMAGE PLATE RIGAKU RAXIS IV mirrors 2003-02-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300 1.5418
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 2.1 50 94.9 0.075 16.8 5.3 111222 111222 -3 24
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) 2.1 2.18 67.2 0.284 2.9 2.9 7770
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 (All) 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 polymerase beta 2.1 19.92 111366 108665 2701 93.2 0.228 0.227 0.227 0.2284 0.26 0.2611 RANDOM 39
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] -1.97 -2.74 4.71
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 21.5 c_scangle_it 3.98 c_scbond_it 2.59 c_mcangle_it 1.96 c_mcbond_it 1.24 c_angle_deg 1.1 c_improper_angle_d 0.87 c_bond_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10199 Nucleic Acid Atoms 1624 Solvent Atoms 1026 Heterogen Atoms 14
Software Software Software Name Purpose CNS refinement SCALEPACK data scaling MOLREP phasing