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Thermoactinomyces vulgaris R-47 alpha-amylase I (TVA I) mutant A357V/Q359N/Y360E (AQY/VNE)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JI1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.1 293 20% MPD, 20% PEG6000, 40 mM MES-NaOH
Crystal Properties Matthews coefficient Solvent content 2.28 46.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.886 α = 90 b = 50.749 β = 103.91 c = 121.897 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 210 2004-11-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1 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 1.5 50 89.5 0.044 12 2 183627
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 1.5 1.58 83.3 0.156 4.6 2
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1JI1 1.5 46.91 174590 9022 89.37 0.1596 0.15833 0.18436 0.1997 RANDOM 13.244
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.992 r_dihedral_angle_4_deg 20.226 r_dihedral_angle_3_deg 11.064 r_dihedral_angle_1_deg 6.448 r_long_range_B_refined 3.896 r_angle_other_deg 3.841 r_long_range_B_other 3.345 r_scangle_other 1.336 r_angle_refined_deg 1.324 r_mcangle_it 0.938
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.992 r_dihedral_angle_4_deg 20.226 r_dihedral_angle_3_deg 11.064 r_dihedral_angle_1_deg 6.448 r_long_range_B_refined 3.896 r_angle_other_deg 3.841 r_long_range_B_other 3.345 r_scangle_other 1.336 r_angle_refined_deg 1.324 r_mcangle_it 0.938 r_mcangle_other 0.938 r_scbond_it 0.885 r_scbond_other 0.885 r_mcbond_it 0.587 r_mcbond_other 0.587 r_chiral_restr 0.083 r_bond_refined_d 0.008 r_gen_planes_other 0.008 r_gen_planes_refined 0.006 r_bond_other_d 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 10072 Nucleic Acid Atoms Solvent Atoms 1952 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling MOLREP phasing