3BLP

Role of aromatic residues in human salivary alpha-amylase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1SMDPDB entry 1SMD

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP929845% MPD, 0.1M Tris.HCl, 10 mM calcium chloride, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.3547.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.085α = 90
b = 74.873β = 90
c = 134.69γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray77CCDADSC QUANTUM 4mirrors2007-11-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCHESS BEAMLINE A10.9777CHESSA1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.65096.20.0930.09320.63.3677196425332
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.61.6392.70.4390.43922.13224

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 1SMD1.630.966771964253340596.250.1950.182020.180750.20532RANDOM23.671
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]
0.240.42-0.66
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.695
r_dihedral_angle_4_deg16.977
r_dihedral_angle_3_deg12.279
r_dihedral_angle_1_deg5.96
r_scangle_it2.917
r_scbond_it1.981
r_angle_refined_deg1.352
r_mcangle_it1.29
r_mcbond_it0.822
r_nbtor_refined0.314
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.695
r_dihedral_angle_4_deg16.977
r_dihedral_angle_3_deg12.279
r_dihedral_angle_1_deg5.96
r_scangle_it2.917
r_scbond_it1.981
r_angle_refined_deg1.352
r_mcangle_it1.29
r_mcbond_it0.822
r_nbtor_refined0.314
r_nbd_refined0.205
r_symmetry_hbond_refined0.158
r_symmetry_vdw_refined0.152
r_xyhbond_nbd_refined0.121
r_chiral_restr0.097
r_metal_ion_refined0.057
r_bond_refined_d0.012
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3937
Nucleic Acid Atoms
Solvent Atoms323
Heterogen Atoms56

Software

Software
Software NamePurpose
REFMACrefinement
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing