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Potato D-enzyme complexed with Acarbose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1X1N
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.6 293 12% PEG 8000, 100 mM HEPES, pH 7.6, 100 mM CaCl2
Crystal Properties Matthews coefficient Solvent content 3.12 60.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.171 α = 90 b = 120.293 β = 90 c = 174.698 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 IMAGE PLATE Bruker DIP-6040 2004-04-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 1.000 SPring-8 BL44XU
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 2.03 60 99.9 0.085 32.3 7.4 46983
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 2.03 2.1 99.7 0.322 7.9 7.5
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 (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 1X1N 2.03 59.96 44986 2414 99.86 0.16542 0.16331 0.1733 0.20563 0.212 RANDOM 32.404
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] 0.04 -0.02 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.317 r_dihedral_angle_4_deg 19.434 r_dihedral_angle_3_deg 13.871 r_long_range_B_refined 7.985 r_long_range_B_other 7.878 r_scangle_other 6.531 r_dihedral_angle_1_deg 6.438 r_scbond_it 4.339 r_scbond_other 4.338 r_mcangle_other 4.106
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.317 r_dihedral_angle_4_deg 19.434 r_dihedral_angle_3_deg 13.871 r_long_range_B_refined 7.985 r_long_range_B_other 7.878 r_scangle_other 6.531 r_dihedral_angle_1_deg 6.438 r_scbond_it 4.339 r_scbond_other 4.338 r_mcangle_other 4.106 r_mcangle_it 4.101 r_mcbond_it 3.143 r_mcbond_other 3.133 r_angle_other_deg 2.334 r_angle_refined_deg 1.693 r_chiral_restr 0.093 r_bond_other_d 0.035 r_gen_planes_other 0.027 r_bond_refined_d 0.012 r_gen_planes_refined 0.011 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4120 Nucleic Acid Atoms Solvent Atoms 455 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling MOLREP phasing PDB_EXTRACT data extraction DENZO data reduction