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Crystal structure of mPNKP catalytic fragment (D170A)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YJ5 PDB ENTRY 1YJ5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 20% PEG 3350, pH 7, vapor diffusion, hanging drop, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.17 43.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.82 α = 90 b = 63.19 β = 88.23 c = 68.12 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 MARMOSAIC 300 mm CCD 2010-07-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.97949 CLSI 08ID-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 1.7 46.3 99.8 0.065 13.91 40013 40013 -3 -3 25.108
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 1.7 1.75 99.8 0.534 2.78
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 PDB ENTRY 1YJ5 1.7 46.3 -3 39992 39992 1999 99.83 0.1627 0.1627 0.161 0.1579 0.195 0.1883 RANDOM 25.227
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] -1.2355 -0.7397 3.7886 -2.5531
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.827 f_angle_d 1.16 f_chiral_restr 0.069 f_bond_d 0.009 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2933 Nucleic Acid Atoms Solvent Atoms 451 Heterogen Atoms 36
Software Software Software Name Purpose XSCALE data scaling PHENIX refinement PDB_EXTRACT data extraction MxDC data collection XDS data reduction PHASER phasing