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Structure of yncA, a putative ACETYLTRANSFERASE from Salmonella typhimurium
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3DR8 PDB ENTRY 3DR8 chain A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 295 20% PEG 5K MME, 0.1 M Bis-Tris, cryoprotected with Paratone-N oil, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.8 56.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 162.898 α = 90 b = 70.229 β = 102.64 c = 59.157 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 IMAGE PLATE RIGAKU RAXIS IV++ Osmic mirrors 2008-05-08 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 1.75 50 93.9 0.047 25.4 3.4 65719 61706 19.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.81 67.1 0.251 5.6 2.6 4362
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 3DR8 chain A 1.75 39.75 61700 58570 3130 93.74 0.16489 0.16301 0.1775 0.20012 0.211 RANDOM 21.209
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 0.02 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.558 r_dihedral_angle_4_deg 13.303 r_dihedral_angle_3_deg 13.026 r_dihedral_angle_1_deg 6.437 r_scangle_it 3.706 r_scbond_it 2.669 r_angle_refined_deg 1.386 r_mcangle_it 1.341 r_mcbond_it 0.936 r_nbtor_refined 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.558 r_dihedral_angle_4_deg 13.303 r_dihedral_angle_3_deg 13.026 r_dihedral_angle_1_deg 6.437 r_scangle_it 3.706 r_scbond_it 2.669 r_angle_refined_deg 1.386 r_mcangle_it 1.341 r_mcbond_it 0.936 r_nbtor_refined 0.3 r_symmetry_vdw_refined 0.206 r_nbd_refined 0.203 r_symmetry_hbond_refined 0.177 r_xyhbond_nbd_refined 0.157 r_chiral_restr 0.109 r_bond_refined_d 0.015 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 4040 Nucleic Acid Atoms Solvent Atoms 811 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection HKL-2000 data reduction HKL-2000 data scaling PHASER phasing