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Structure determination and refinement at 1.8 A resolution of Disproportionating Enzyme from Potato
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1WW0 PDB ENTRY 1WW0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 277 PEG 8000, HEPES, calcium chloride, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.1 60
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.869 α = 90 b = 120.535 β = 90 c = 174.382 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 100 CCD ADSC QUANTUM 210 2004-11-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0000 Photon Factory AR-NW12A
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 1.8 87.04 89.8 0.031 7 68303 61336 23.13
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 1.8 1.9 55.9 0.144 11 5.4 5475
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1WW0 1.8 87.04 61323 58187 3136 89.6 0.19 0.1806 0.17901 0.1775 0.21002 0.2081 RANDOM 25.409
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] 1.01 -0.31 -0.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.464 r_dihedral_angle_4_deg 18.268 r_dihedral_angle_3_deg 12.586 r_dihedral_angle_1_deg 5.316 r_scangle_it 2.772 r_scbond_it 1.736 r_mcangle_it 1.318 r_angle_refined_deg 1.15 r_mcbond_it 0.793 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.464 r_dihedral_angle_4_deg 18.268 r_dihedral_angle_3_deg 12.586 r_dihedral_angle_1_deg 5.316 r_scangle_it 2.772 r_scbond_it 1.736 r_mcangle_it 1.318 r_angle_refined_deg 1.15 r_mcbond_it 0.793 r_nbtor_refined 0.304 r_nbd_refined 0.188 r_symmetry_hbond_refined 0.177 r_symmetry_vdw_refined 0.173 r_metal_ion_refined 0.161 r_xyhbond_nbd_refined 0.134 r_chiral_restr 0.082 r_bond_refined_d 0.01 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4183 Nucleic Acid Atoms Solvent Atoms 662 Heterogen Atoms 55
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling MOLREP phasing