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Crystal structure of calcium free alpha amylase from Bacillus sp. strain KSM-K38 (AmyK38, in calcium containing solution)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UD2 Model of AmyK38 wild-type structure
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.4 293 MPD, PEG 4000, sodium citrate, calcium chloride, Tris-HCl, pH 6.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.61 65.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 133.731 α = 90 b = 133.731 β = 90 c = 133.731 γ = 90
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 4 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL40B2 0.9780 SPring-8 BL40B2
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 2.15 100 100 0.157 11.7 11 43599 43599 12.3
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) 2.15 2.23 100 0.3 4.43 4349
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-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT Model of AmyK38 wild-type structure 2.15 77.21 43569 43087 2129 98.8 0.192 0.221 RANDOM 16
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 c_dihedral_angle_d 23.2 c_scangle_it 3.11 c_scbond_it 2.48 c_mcangle_it 2.12 c_mcbond_it 1.58 c_angle_deg 1.3 c_improper_angle_d 0.71 c_bond_d 0.006 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.2 c_scangle_it 3.11 c_scbond_it 2.48 c_mcangle_it 2.12 c_mcbond_it 1.58 c_angle_deg 1.3 c_improper_angle_d 0.71 c_bond_d 0.006 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3908 Nucleic Acid Atoms Solvent Atoms 290 Heterogen Atoms 3
Software Software Software Name Purpose CNS refinement HKL-2000 data reduction SCALEPACK data scaling AMoRE phasing