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Crystal structure of a GNAT superfamily acetyltransferase PA4794 in complex with bisubstrate analog 3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4L8A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 289 2M ammonium sulfate, 0.1M Bis Tris pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.38 48.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.335 α = 90 b = 76.121 β = 90 c = 39.149 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 CCD MARMOSAIC 300 mm CCD Beryllium Lenses 2014-12-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.9786 APS 21-ID-G
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 1.4 50 99.9 0.053 0.057 0.022 9.8 6.9 34368
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 1.4 1.42 100 0.8 0.867 0.33 0.777 6.8 1669
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 4L8A 1.4 45.8 32591 1734 99.76 0.1464 0.1451 0.1476 0.1704 0.1738 RANDOM 20.311
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] 1.61 -0.62 -0.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.7 r_sphericity_free 25.309 r_sphericity_bonded 12.899 r_dihedral_angle_4_deg 12.569 r_dihedral_angle_3_deg 11.709 r_rigid_bond_restr 9.227 r_dihedral_angle_1_deg 5.379 r_angle_other_deg 1.972 r_angle_refined_deg 1.231 r_chiral_restr 0.077
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.7 r_sphericity_free 25.309 r_sphericity_bonded 12.899 r_dihedral_angle_4_deg 12.569 r_dihedral_angle_3_deg 11.709 r_rigid_bond_restr 9.227 r_dihedral_angle_1_deg 5.379 r_angle_other_deg 1.972 r_angle_refined_deg 1.231 r_chiral_restr 0.077 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_gen_planes_other 0.003 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1233 Nucleic Acid Atoms Solvent Atoms 188 Heterogen Atoms 131
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling PDB_EXTRACT data extraction HKL-3000 data scaling HKL-3000 data reduction HKL-3000 phasing DENZO data reduction SCALEPACK data scaling