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Crystal structure of predicted N-acyltransferase (ypeA) in complex with acetyl-CoA from Escherichia coli
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3PDO PDB ENTRY 3PDO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 292 0.2 M lithium sulfate, 25% w/v PEG3350, 0.1 M Bis-Tris, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 2.25 45.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.334 α = 90 b = 139.968 β = 112.11 c = 75.358 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 mirrors 2014-07-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 0.97910 APS 21-ID-D
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 1.948 69.984 98.6 0.073 33.8 4.6 92573 92573 -3 53.2
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 1.948 1.98 95.2 0.46 2.05 3.9 4492
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 3PDO 1.948 69.98 87793 87793 4600 98.06 0.19033 0.18813 0.1966 0.23236 0.2322 RANDOM 55.082
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] -0.41 1.17 1.85 -1.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.113 r_dihedral_angle_4_deg 13.993 r_dihedral_angle_3_deg 12.218 r_long_range_B_refined 8.399 r_long_range_B_other 8.376 r_scangle_other 6.582 r_scbond_it 4.895 r_scbond_other 4.813 r_mcangle_it 4.027 r_mcangle_other 4.026
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.113 r_dihedral_angle_4_deg 13.993 r_dihedral_angle_3_deg 12.218 r_long_range_B_refined 8.399 r_long_range_B_other 8.376 r_scangle_other 6.582 r_scbond_it 4.895 r_scbond_other 4.813 r_mcangle_it 4.027 r_mcangle_other 4.026 r_mcbond_it 3.337 r_mcbond_other 3.278 r_dihedral_angle_1_deg 2.878 r_angle_refined_deg 1.871 r_angle_other_deg 0.832 r_chiral_restr 0.117 r_gen_planes_refined 0.023 r_gen_planes_other 0.018 r_bond_refined_d 0.013 r_bond_other_d 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9140 Nucleic Acid Atoms Solvent Atoms 243 Heterogen Atoms 458
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling