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Crystal Structure of PaaK2 in complex with phenylacetyl adenylate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Y4N PDB ENTRY 2Y4N
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 PROTEIN INCUBATED IN 3 MM MGCL2, ATP, AND 5 MM PHENYLACETIC ACID FOR 1 HR AND CRYSTALLIZED IN 17% (W/V) PEG 6000, 0.1 M HEPES PH 7.5, 0.1 M KCL AND 2.5% GLYCEROL.
Crystal Properties Matthews coefficient Solvent content 2.37 48.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.15 α = 90 b = 81.97 β = 97.27 c = 80.89 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 MARRESEARCH M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 SSRL BL9-2
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 1.9 30 96 0.09 9.2 4.1 69914 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 1.9 2 92.9 0.33 3.1 3.1
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 (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 2Y4N 1.9 40.99 66361 3532 98.91 0.16807 0.16558 0.1664 0.21404 0.2146 RANDOM 20.917
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.206 r_dihedral_angle_4_deg 18.494 r_dihedral_angle_3_deg 16.813 r_dihedral_angle_1_deg 7.855 r_scangle_it 5.826 r_scbond_it 3.967 r_mcangle_it 2.246 r_mcbond_it 1.496 r_angle_refined_deg 0.962 r_chiral_restr 0.085
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.206 r_dihedral_angle_4_deg 18.494 r_dihedral_angle_3_deg 16.813 r_dihedral_angle_1_deg 7.855 r_scangle_it 5.826 r_scbond_it 3.967 r_mcangle_it 2.246 r_mcbond_it 1.496 r_angle_refined_deg 0.962 r_chiral_restr 0.085 r_gen_planes_refined 0.017 r_bond_refined_d 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6647 Nucleic Acid Atoms Solvent Atoms 860 Heterogen Atoms 104
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling MOLREP phasing