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Crystal structure of a protein acetyltransferase, HP0935
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Model obtained by experimental phasing (iodine SAD) at 2.40A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 277 0.2M potassium thiocyanate, 0.1M Bis-Tris propane pH 6.5, 20% (w/v) polyethylene glycol 3500, 20% (w/v) ethylene glycol (cryo, soaked)
Crystal Properties Matthews coefficient Solvent content 2.47 50.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.856 α = 90 b = 66.17 β = 91.42 c = 70.904 γ = 90
Symmetry Space Group C 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 CMOS BRUKER PHOTON 100 2018-08-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR 1.5418
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 70.88 99.8 0.12 0.129 0.045 0.996 10.4 7.4 36953
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 2.05 100 0.586 0.652 0.283 0.792 5.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2 70.88 35062 1880 99.82 0.2169 0.2152 0.2218 0.2463 0.2525 RANDOM 21.815
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] -0.46 -0.22 0.41 0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.422 r_dihedral_angle_2_deg 11.099 r_dihedral_angle_1_deg 6.976 r_mcangle_it 2.253 r_angle_refined_deg 1.898 r_mcbond_it 1.62 r_mcbond_other 1.589 r_angle_other_deg 0.699 r_chiral_restr 0.099 r_bond_refined_d 0.014
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.422 r_dihedral_angle_2_deg 11.099 r_dihedral_angle_1_deg 6.976 r_mcangle_it 2.253 r_angle_refined_deg 1.898 r_mcbond_it 1.62 r_mcbond_other 1.589 r_angle_other_deg 0.699 r_chiral_restr 0.099 r_bond_refined_d 0.014 r_gen_planes_refined 0.013 r_bond_other_d 0.004 r_gen_planes_other 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3603 Nucleic Acid Atoms Solvent Atoms 282 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PHASER phasing PDB_EXTRACT data extraction PROTEUM PLUS data reduction