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Crystal structure of Grenache (Vitis vinifera) Polyphenol Oxidase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BT1 Polyphenol oxidase of sweet potato (1BT1)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 291 0.2 M Ammonium acetate, 0.1 M Sodium citrate tribasic dihydrate pH 5.6, 30% w/v Polyethylene glycol 4,000, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 3.31 62.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.03 α = 90 b = 120.77 β = 90 c = 140.8 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 298 CCD ADSC QUANTUM 210 Monochromator 2006-06-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X6A 1.1 NSLS X6A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.2 50 6.96 26382
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) 2.2 2.28 97.8 0.487 2.9 5.41 26382
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 (All) 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 Polyphenol oxidase of sweet potato (1BT1) 2.2 37.06 23748 2598 99.75 0.2057 0.20572 0.20053 0.1932 0.25205 0.2383 RANDOM 39.449
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
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.535 r_dihedral_angle_3_deg 20.474 r_dihedral_angle_4_deg 18.507 r_dihedral_angle_1_deg 18.187 r_scangle_it 4.867 r_scbond_it 3.27 r_angle_refined_deg 2.545 r_mcangle_it 2.153 r_mcbond_it 1.313 r_nbtor_refined 0.317
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.535 r_dihedral_angle_3_deg 20.474 r_dihedral_angle_4_deg 18.507 r_dihedral_angle_1_deg 18.187 r_scangle_it 4.867 r_scbond_it 3.27 r_angle_refined_deg 2.545 r_mcangle_it 2.153 r_mcbond_it 1.313 r_nbtor_refined 0.317 r_chiral_restr 0.277 r_nbd_refined 0.247 r_symmetry_vdw_refined 0.23 r_symmetry_hbond_refined 0.2 r_xyhbond_nbd_refined 0.161 r_bond_refined_d 0.024 r_metal_ion_refined 0.01 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2713 Nucleic Acid Atoms Solvent Atoms 128 Heterogen Atoms 3
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection CrystalClear data reduction d*TREK data scaling MOLREP phasing