3BCD

Alpha-amylase B in complex with maltotetraose and alpha-cyclodextrin


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3BC9PDB ENTRY 3BC9

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP62980.2M sodium acetate, 0.1M Mes-OH, 20% (w/v) PEG 8000, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
3.2662.22

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 228.7α = 90
b = 78.05β = 98.9
c = 50.64γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mmmirrors2007-02-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX II BEAMLINE I911-21.0412MAX III911-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.153097.90.057183.84708047080
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.152.2960.4633.63.4

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB ENTRY 3BC92.230430894308989898.150.196850.195950.24008RANDOM9.137
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]
0.190.381.16-1.23
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.667
r_dihedral_angle_4_deg17.689
r_dihedral_angle_3_deg16.556
r_dihedral_angle_1_deg6.77
r_scangle_it3.526
r_scbond_it2.352
r_angle_refined_deg1.939
r_angle_other_deg1.597
r_mcangle_it1.493
r_mcbond_it1.013
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.667
r_dihedral_angle_4_deg17.689
r_dihedral_angle_3_deg16.556
r_dihedral_angle_1_deg6.77
r_scangle_it3.526
r_scbond_it2.352
r_angle_refined_deg1.939
r_angle_other_deg1.597
r_mcangle_it1.493
r_mcbond_it1.013
r_metal_ion_refined0.299
r_mcbond_other0.228
r_nbd_refined0.218
r_nbd_other0.207
r_nbtor_refined0.195
r_xyhbond_nbd_refined0.182
r_symmetry_vdw_other0.171
r_symmetry_hbond_refined0.135
r_symmetry_vdw_refined0.128
r_chiral_restr0.115
r_nbtor_other0.095
r_xyhbond_nbd_other0.044
r_bond_refined_d0.022
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4747
Nucleic Acid Atoms
Solvent Atoms259
Heterogen Atoms164

Software

Software
Software NamePurpose
REFMACrefinement
MAR345data collection
XDSdata reduction
XSCALEdata scaling
REFMACphasing