2GUY

Orthorhombic crystal structure (space group P21212) of Aspergillus niger alpha-amylase at 1.6 A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7TAAPDB ENTRY 7TAA

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.829630% PEG 8000, 0.2M Na-acetate, 0.1M Na-cacodylate, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Crystal Properties
Matthews coefficientSolvent content
2.346.58

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 102.799α = 90
b = 63.228β = 90
c = 74.456γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152005-08-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.91835ESRFID23-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.594098.60.0796513065130
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.591.6690.10.556

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 7TAA1.59206071160711324596.880.165270.165270.163620.19623RANDOM26.31
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]
-0.791.08-0.29
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.711
r_dihedral_angle_3_deg13.725
r_dihedral_angle_4_deg10.104
r_dihedral_angle_1_deg5.772
r_scangle_it2.129
r_mcangle_it1.726
r_angle_refined_deg1.483
r_scbond_it1.482
r_mcbond_it1.158
r_nbtor_refined0.324
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.711
r_dihedral_angle_3_deg13.725
r_dihedral_angle_4_deg10.104
r_dihedral_angle_1_deg5.772
r_scangle_it2.129
r_mcangle_it1.726
r_angle_refined_deg1.483
r_scbond_it1.482
r_mcbond_it1.158
r_nbtor_refined0.324
r_symmetry_hbond_refined0.279
r_symmetry_vdw_refined0.235
r_nbd_refined0.217
r_xyhbond_nbd_refined0.172
r_chiral_restr0.11
r_metal_ion_refined0.03
r_bond_refined_d0.014
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3686
Nucleic Acid Atoms
Solvent Atoms564
Heterogen Atoms40

Software

Software
Software NamePurpose
REFMACrefinement
ProDCdata collection
SCALEPACKdata scaling
PHASERphasing