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Orthorhombic crystal structure (space group P21212) of Aspergillus niger alpha-amylase at 1.6 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7TAA PDB ENTRY 7TAA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.8 296 30% PEG 8000, 0.2M Na-acetate, 0.1M Na-cacodylate, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Crystal Properties Matthews coefficient Solvent content 2.3 46.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.799 α = 90 b = 63.228 β = 90 c = 74.456 γ = 90
Symmetry Space Group P 21 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 2005-08-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.91835 ESRF ID23-1
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 1.59 40 98.6 0.079 65130 65130
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 1.59 1.66 90.1 0.556
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-Factor (All) 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 PDB ENTRY 7TAA 1.59 20 60711 60711 3245 96.88 0.16527 0.16527 0.16362 0.1712 0.19623 0.2012 RANDOM 26.31
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] -0.79 1.08 -0.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.711 r_dihedral_angle_3_deg 13.725 r_dihedral_angle_4_deg 10.104 r_dihedral_angle_1_deg 5.772 r_scangle_it 2.129 r_mcangle_it 1.726 r_angle_refined_deg 1.483 r_scbond_it 1.482 r_mcbond_it 1.158 r_nbtor_refined 0.324
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.711 r_dihedral_angle_3_deg 13.725 r_dihedral_angle_4_deg 10.104 r_dihedral_angle_1_deg 5.772 r_scangle_it 2.129 r_mcangle_it 1.726 r_angle_refined_deg 1.483 r_scbond_it 1.482 r_mcbond_it 1.158 r_nbtor_refined 0.324 r_symmetry_hbond_refined 0.279 r_symmetry_vdw_refined 0.235 r_nbd_refined 0.217 r_xyhbond_nbd_refined 0.172 r_chiral_restr 0.11 r_metal_ion_refined 0.03 r_bond_refined_d 0.014 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3686 Nucleic Acid Atoms Solvent Atoms 564 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement ProDC data collection SCALEPACK data scaling PHASER phasing