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Puromycin N-acetyltransferase in complex with acetylated puromycin and CoA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7K09
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.26 281 9.9% (w/v) 1,6-hexanediol, 1.59 M ammonium sulfate, 7.4 % (v/v) polyethylene glycol 400, 0.1 M HEPES pH 8.26, 0.5 n-hexyl-b-D-glucopyranoside
Crystal Properties Matthews coefficient Solvent content 2.79 55.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.596 α = 90 b = 141.509 β = 100.341 c = 98.985 γ = 90
Symmetry Space Group I 1 2 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 ADSC QUANTUM 315r 2016-03-11 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD ADSC QUANTUM 315r 2016-03-11 M SINGLE WAVELENGTH 3 1 x-ray 100 CCD ADSC QUANTUM 315r 2016-04-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.9537 Australian Synchrotron MX2 2 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.9537 Australian Synchrotron MX2 3 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.9537 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 70.75 99.9 0.376 0.4 0.136 0.989 7.7 17.2 33396
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.05 99.4 0.608 0.857 2.3 15.2
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 (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 7K09 2 42.488 33371 1619 99.97 0.209 0.2071 0.2405 0.2413 16.23
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] -1.713 0.798 -2.055 3.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.425 r_dihedral_angle_4_deg 15.643 r_dihedral_angle_3_deg 13.779 r_dihedral_angle_1_deg 6.514 r_lrange_it 6.204 r_lrange_other 6.109 r_scangle_it 3.355 r_scangle_other 3.234 r_scbond_it 2.201 r_scbond_other 2.092
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.425 r_dihedral_angle_4_deg 15.643 r_dihedral_angle_3_deg 13.779 r_dihedral_angle_1_deg 6.514 r_lrange_it 6.204 r_lrange_other 6.109 r_scangle_it 3.355 r_scangle_other 3.234 r_scbond_it 2.201 r_scbond_other 2.092 r_mcangle_it 2.023 r_mcangle_other 2.023 r_angle_refined_deg 1.621 r_angle_other_deg 1.331 r_mcbond_it 1.268 r_mcbond_other 1.263 r_nbd_refined 0.213 r_nbd_other 0.196 r_xyhbond_nbd_refined 0.192 r_symmetry_nbd_other 0.183 r_symmetry_xyhbond_nbd_refined 0.182 r_symmetry_nbd_refined 0.163 r_nbtor_refined 0.162 r_symmetry_xyhbond_nbd_other 0.13 r_symmetry_nbtor_other 0.083 r_chiral_restr 0.082 r_ncsr_local_group_1 0.069 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2968 Nucleic Acid Atoms Solvent Atoms 273 Heterogen Atoms 226
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing