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Structure of Peptidyl-alpha-hydroxyglycine alpha-Amidating Lyase (PAL) bound to alpha-hydroxyhippuric acid (non-peptidic substrate)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other PALcc native, being deposited at the same time as this structure
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.8 293 0.1M sodium acetate pH=4.8, 0.5mM mercury(II) acetate - 0.2ml mother liquor in reservoir. Then, crystals soaked in 5mM hydroxyhippuric acid for several hours, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.56 51.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.93 α = 90 b = 75.08 β = 90 c = 97.026 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 MAR CCD 165 mm Monochromator Kohzu HLD-4 Double Crystal 2008-07-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 1.00724 APS 31-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.5 59.34 99.6 0.075 23.5 6.8 13347 13347
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) 2.5 2.59 98.9 0.48 2.7 5.7 1306
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 PALcc native, being deposited at the same time as this structure 2.52 59.34 13347 12648 655 99.09 0.20939 0.20672 0.2578 0.26019 0.3026 RANDOM 44.912
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] 1.12 0.24 -1.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.247 r_dihedral_angle_4_deg 19.785 r_dihedral_angle_3_deg 17.925 r_dihedral_angle_1_deg 7.552 r_angle_refined_deg 1.246 r_scangle_it 1.237 r_scbond_it 1.213 r_mcangle_it 0.541 r_nbtor_refined 0.31 r_mcbond_it 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.247 r_dihedral_angle_4_deg 19.785 r_dihedral_angle_3_deg 17.925 r_dihedral_angle_1_deg 7.552 r_angle_refined_deg 1.246 r_scangle_it 1.237 r_scbond_it 1.213 r_mcangle_it 0.541 r_nbtor_refined 0.31 r_mcbond_it 0.31 r_symmetry_hbond_refined 0.224 r_nbd_refined 0.195 r_symmetry_vdw_refined 0.167 r_xyhbond_nbd_refined 0.126 r_chiral_restr 0.115 r_bond_refined_d 0.008 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2619 Nucleic Acid Atoms Solvent Atoms 118 Heterogen Atoms 17
Software Software Software Name Purpose AMoRE phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling