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Crystal Structure of human DNA polymerase lambda L431A mutant in complex with a one nucleotide DNA gap and dCTP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3MGI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 277 0.15 M Potassium Bromide, 30% Polyethylene Glycol Monomethyl ether 2000
Crystal Properties Matthews coefficient Solvent content 3.48 69.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.003 α = 90 b = 148.712 β = 90 c = 86.414 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 95 CCD RAYONIX MX300HE 2014-09-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL13B1 1.00000 NSRRC BL13B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 30 98.7 0.091 0.1 0.042 9.1 5.5 41766 29.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.59 92.8 0.32 0.354 0.148 0.939 5.2 3872
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3MGI 2.5 28.123 1.36 41640 1985 98.68 0.2035 0.2019 0.2056 0.2335 0.2316
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 18.566 f_angle_d 0.738 f_chiral_restr 0.028 f_bond_d 0.004 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5071 Nucleic Acid Atoms 854 Solvent Atoms 307 Heterogen Atoms 60
Software Software Software Name Purpose PHENIX refinement HKL-2000 data collection HKL-2000 data scaling PDB_EXTRACT data extraction HKL-2000 data reduction PHENIX phasing