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Structure of yncA, a putative ACETYLTRANSFERASE from Salmonella typhimurium with its cofactor Acetyl-CoA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BL1 molecule A of 2BL1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.6 295 1.4 M Sodium Acetate trihydrate 5.6 pH plus 5 mM Acetyl Coenzyme A, cryoprotected with N-paratone oil, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.12 42.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.254 α = 90 b = 71.374 β = 90 c = 74.005 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV++ Osmic mirrors 2008-04-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.54178
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 1.86 50 98 0.085 21 6.4 28962 28378
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) 1.86 1.93 96 0.471 5.3 6.3
Refinement Statistics Diffraction ID Structure Solution 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT molecule A of 2BL1 1.95 47.35 24632 1255 98.3 0.157 0.154 0.162 0.216 0.2224 20.38
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] -0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.9 r_dihedral_angle_3_deg 14.169 r_dihedral_angle_4_deg 11.808 r_dihedral_angle_1_deg 7.071 r_scangle_it 3.531 r_scbond_it 2.52 r_angle_refined_deg 1.577 r_mcangle_it 1.359 r_mcbond_it 0.861 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.9 r_dihedral_angle_3_deg 14.169 r_dihedral_angle_4_deg 11.808 r_dihedral_angle_1_deg 7.071 r_scangle_it 3.531 r_scbond_it 2.52 r_angle_refined_deg 1.577 r_mcangle_it 1.359 r_mcbond_it 0.861 r_nbtor_refined 0.301 r_symmetry_vdw_refined 0.221 r_symmetry_hbond_refined 0.209 r_nbd_refined 0.202 r_xyhbond_nbd_refined 0.156 r_chiral_restr 0.111 r_bond_refined_d 0.017 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2733 Nucleic Acid Atoms Solvent Atoms 387 Heterogen Atoms 126
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection HKL-2000 data reduction HKL-2000 data scaling PHASER phasing