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PylD cocrystallized with L-Lysine-Ne-3S-methyl-L-ornithine and NAD+
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4Q39 pdb entry 4Q39
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 0.1 M TRIS, 27% PEG3350, 0.2 M NaCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.47 50.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.49 α = 90 b = 259.85 β = 90 c = 48.66 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 100 PIXEL PSI PILATUS 6M 2012-11-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.0 SLS X06SA
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 2.2 40 99.5 0.079 15.3 4.4 57676 57408 2 2
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 2.2 2.3 99.8 0.551 3.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Number Reflections (All) 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 4Q39 2.2 15 2 57355 54490 2865 99.58 0.17112 0.16936 0.1779 0.20448 0.2098 RANDOM 43.118
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] -0.8 0.86 -0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.522 r_dihedral_angle_3_deg 15.668 r_dihedral_angle_4_deg 14.84 r_long_range_B_refined 5.646 r_long_range_B_other 5.527 r_dihedral_angle_1_deg 5.435 r_scangle_other 2.066 r_mcangle_it 1.837 r_mcangle_other 1.837 r_scbond_it 1.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.522 r_dihedral_angle_3_deg 15.668 r_dihedral_angle_4_deg 14.84 r_long_range_B_refined 5.646 r_long_range_B_other 5.527 r_dihedral_angle_1_deg 5.435 r_scangle_other 2.066 r_mcangle_it 1.837 r_mcangle_other 1.837 r_scbond_it 1.35 r_scbond_other 1.35 r_angle_refined_deg 1.273 r_mcbond_it 1.064 r_mcbond_other 1.064 r_angle_other_deg 0.748 r_chiral_restr 0.065 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7826 Nucleic Acid Atoms Solvent Atoms 326 Heterogen Atoms 423
Software Software Software Name Purpose XDS data scaling PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling