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Thermoactinomyces vulgaris R-47 alpha-amylase I (TVA I) 11 residues (from A363 to N373) deletion mutant (Del11)
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 45.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.972 α = 90 b = 54.022 β = 100.07 c = 77.907 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 1.37 50 92.3 0.048 14.1 2.7 121625
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 1.37 1.44 83.8 0.168 5.1 2.4
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 1.37 49.74 115635 5972 91.88 0.13831 0.13768 0.1502 0.1699 RANDOM 10.487
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 35.825 r_dihedral_angle_4_deg 21.875 r_dihedral_angle_3_deg 10.73 r_dihedral_angle_1_deg 6.513 r_long_range_B_refined 3.6 r_long_range_B_other 3.036 r_angle_refined_deg 1.352 r_scangle_other 1.174 r_angle_other_deg 0.954 r_mcangle_it 0.828
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.825 r_dihedral_angle_4_deg 21.875 r_dihedral_angle_3_deg 10.73 r_dihedral_angle_1_deg 6.513 r_long_range_B_refined 3.6 r_long_range_B_other 3.036 r_angle_refined_deg 1.352 r_scangle_other 1.174 r_angle_other_deg 0.954 r_mcangle_it 0.828 r_mcangle_other 0.828 r_scbond_it 0.782 r_scbond_other 0.782 r_mcbond_it 0.503 r_mcbond_other 0.503 r_chiral_restr 0.087 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.002 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 4965 Nucleic Acid Atoms Solvent Atoms 916 Heterogen Atoms 11
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling MOLREP phasing