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alliinase from allium sativum (garlic)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LK9 PDB ENTRY 1LK9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 293 PEG 4000, AMMONIUM ACETATE, TRI- SODIUM CITRATE, PH 5.6, pH 5.60, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.24 44.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.665 α = 90 b = 126.892 β = 97.3 c = 102.664 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 ADSC QUANTUM 4 2003-06-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 0.933 ESRF ID14-2
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 1.39 46.1 95.7 0.049 0.049 40.4 3.08 327315 327315 -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 1.39 1.41 78.1 0.598 0.598 2.1 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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1LK9 1.4 46.1 327315 310776 16535 96.47 0.16914 0.16724 0.1766 0.20452 RANDOM 17.133
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] -0.03 0.44 -0.45 0.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.808 r_sphericity_free 25.393 r_dihedral_angle_4_deg 15.317 r_dihedral_angle_3_deg 12.538 r_sphericity_bonded 10.818 r_rigid_bond_restr 6.646 r_dihedral_angle_1_deg 6.113 r_scangle_it 5.987 r_scbond_it 4.542 r_mcangle_it 2.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.808 r_sphericity_free 25.393 r_dihedral_angle_4_deg 15.317 r_dihedral_angle_3_deg 12.538 r_sphericity_bonded 10.818 r_rigid_bond_restr 6.646 r_dihedral_angle_1_deg 6.113 r_scangle_it 5.987 r_scbond_it 4.542 r_mcangle_it 2.86 r_mcbond_it 2.554 r_angle_refined_deg 1.728 r_angle_other_deg 0.991 r_mcbond_other 0.529 r_symmetry_vdw_other 0.284 r_symmetry_vdw_refined 0.241 r_symmetry_hbond_refined 0.227 r_nbd_refined 0.221 r_xyhbond_nbd_refined 0.211 r_nbd_other 0.2 r_nbtor_refined 0.189 r_chiral_restr 0.109 r_nbtor_other 0.093 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 r_gen_planes_other 0.005 r_bond_other_d 0.002 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13748 Nucleic Acid Atoms Solvent Atoms 2669 Heterogen Atoms 408
Software Software Software Name Purpose MOLREP phasing REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling