1MFU

Probing the role of a mobile loop in human salivary amylase: Structural studies on the loop-deleted mutant


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1JXKPDB entry 1jxk

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1soaking with acarbose at 1 mM concentration for 24 hours929840% mpd, pH 9.0, soaking with acarbose at 1 mM concentration for 24 hours, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.3447.53

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.074α = 90
b = 73.815β = 90
c = 135.787γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 4monochromator2002-03-31MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCHESS BEAMLINE F10.91CHESSF1

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
1226.5496.80.060.0624.54.835031350311125.6
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)
22.070.2670.26773488

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 1jxk226.543503133226174696.860.16220.162260.160110.20109RANDOM25.789
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
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.254
r_scangle_it2.997
r_scbond_it2.041
r_angle_refined_deg1.368
r_mcangle_it1.265
r_mcbond_it0.691
r_nbd_refined0.2
r_symmetry_vdw_refined0.199
r_symmetry_hbond_refined0.142
r_xyhbond_nbd_refined0.139
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.254
r_scangle_it2.997
r_scbond_it2.041
r_angle_refined_deg1.368
r_mcangle_it1.265
r_mcbond_it0.691
r_nbd_refined0.2
r_symmetry_vdw_refined0.199
r_symmetry_hbond_refined0.142
r_xyhbond_nbd_refined0.139
r_chiral_restr0.096
r_metal_ion_refined0.077
r_bond_refined_d0.013
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3924
Nucleic Acid Atoms
Solvent Atoms290
Heterogen Atoms199

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement