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succinyl-AAPK-trypsin acyl-enzyme at 1.28 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2AGE PDB entry 2AGE with ligand and solvent removed
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 298 ammonium sulfate, bis-tris propane, calcium chloride, benzamidine, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.81 55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.388 α = 90 b = 63.588 β = 90 c = 68.849 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 CCD ADSC QUANTUM 4 2005-05-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.00000 ALS 8.3.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.28 46.63 96.27 0.075 0.075 9.3 3.1 59870 59870 -3 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.28 1.35 51.9 0.475 0.475 1.7 2.2
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 (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 2AGE with ligand and solvent removed 1.28 46.63 59869 59869 3027 96.27 0.125 0.125 0.124 0.158 0.1844 inherited from PDB entry 2AGE 8.963
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] 0.83 -0.74 -0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.459 r_dihedral_angle_4_deg 20.84 r_sphericity_free 16.795 r_dihedral_angle_3_deg 10.63 r_sphericity_bonded 7.134 r_scangle_it 6.747 r_dihedral_angle_1_deg 6.679 r_scbond_it 5.464 r_rigid_bond_restr 5.198 r_mcangle_it 4.354
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.459 r_dihedral_angle_4_deg 20.84 r_sphericity_free 16.795 r_dihedral_angle_3_deg 10.63 r_sphericity_bonded 7.134 r_scangle_it 6.747 r_dihedral_angle_1_deg 6.679 r_scbond_it 5.464 r_rigid_bond_restr 5.198 r_mcangle_it 4.354 r_mcbond_it 3.455 r_mcbond_other 2.264 r_angle_refined_deg 1.742 r_angle_other_deg 0.933 r_nbd_refined 0.386 r_symmetry_vdw_other 0.325 r_symmetry_hbond_refined 0.283 r_nbd_other 0.264 r_xyhbond_nbd_refined 0.22 r_metal_ion_refined 0.143 r_chiral_restr 0.125 r_nbtor_other 0.094 r_symmetry_vdw_refined 0.032 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 r_bond_other_d 0.006 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1648 Nucleic Acid Atoms Solvent Atoms 357 Heterogen Atoms 6
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling EPMR phasing REFMAC refinement CCP4 data scaling