1JXJ

Role of mobile loop in the mechanism of human salivary 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 DROP9298MPD, calcium chloride, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K, temperature 298.0K
Crystal Properties
Matthews coefficientSolvent content
2.2444.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.295α = 90
b = 75.25β = 90
c = 135.018γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray200IMAGE PLATERIGAKU RAXIS IVmirrors2001-03-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.5418

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
11.9965.9497.70.0620.05116.23.23628834452223
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)
1.992.07950.0620.2813

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 1SMD1.9965.943445234452179597.70.16610.166150.164480.19835RANDOM22.987
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_deg4.826
r_scangle_it3.419
r_scbond_it2.299
r_angle_refined_deg1.617
r_mcangle_it1.412
r_mcbond_it0.798
r_xyhbond_nbd_refined0.22
r_chiral_restr0.129
r_dihedral_angle_3_deg0.129
r_xyhbond_nbd_other0.123
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg4.826
r_scangle_it3.419
r_scbond_it2.299
r_angle_refined_deg1.617
r_mcangle_it1.412
r_mcbond_it0.798
r_xyhbond_nbd_refined0.22
r_chiral_restr0.129
r_dihedral_angle_3_deg0.129
r_xyhbond_nbd_other0.123
r_bond_refined_d0.015
r_gen_planes_refined0.007
r_nbtor_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3940
Nucleic Acid Atoms
Solvent Atoms294
Heterogen Atoms2

Software

Software
Software NamePurpose
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement