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Amylase in complex with acarbose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1WP6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 0.2 M Na citrate, 0.1 M BTP pH 6.5, 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.97 58.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 180.9 α = 90 b = 180.9 β = 90 c = 77.85 γ = 90
Symmetry Space Group P 41 21 2
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 315 2013-02-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.98 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) 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 2.07 57.21 99.6 0.17 0.18 1 16.7 14.5 78951
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.07 2.12 100 0.74 0.8 0.907 14.8
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 1WP6 2.07 57.21 74920 3965 99.99 0.14016 0.13825 0.1503 0.17617 0.1848 RANDOM 18.404
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] 0.49 0.49 -0.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.729 r_dihedral_angle_1_deg 16.265 r_dihedral_angle_3_deg 12.469 r_dihedral_angle_4_deg 10.518 r_long_range_B_refined 7.659 r_long_range_B_other 7.544 r_scangle_other 2.622 r_scbond_it 1.823 r_scbond_other 1.823 r_mcangle_it 1.741
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.729 r_dihedral_angle_1_deg 16.265 r_dihedral_angle_3_deg 12.469 r_dihedral_angle_4_deg 10.518 r_long_range_B_refined 7.659 r_long_range_B_other 7.544 r_scangle_other 2.622 r_scbond_it 1.823 r_scbond_other 1.823 r_mcangle_it 1.741 r_mcangle_other 1.741 r_angle_refined_deg 1.664 r_angle_other_deg 1.445 r_mcbond_it 1.255 r_mcbond_other 1.254 r_chiral_restr 0.091 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.005 r_gen_planes_other 0.001 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 7576 Nucleic Acid Atoms Solvent Atoms 1089 Heterogen Atoms 280
Software Software Software Name Purpose REFMAC refinement Aimless data scaling BUCCANEER model building MOLREP phasing Coot model building