2XFR | pdb_00002xfr

Crystal structure of barley beta-amylase at atomic resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1B1YPDB ENTRY 1B1Y

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.5291CRYSTALS WERE GROWN AT 291 K USING THE HANGING DROP VAPOUR DIFFUSION METHOD WITH PROTEIN AT 10 MG PER ML AND A PRECIPITANT COMPRISED OF 14 PERCENT PEG 3350 IN 100 MM BIS-TRIS PROPANE BUFFER AT PH 5.5
Crystal Properties
Matthews coefficientSolvent content
1.9135.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.83α = 90
b = 71.338β = 90
c = 92.659γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2008-03-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I02DiamondI02

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
10.9549.5394.60.12.325.28253864-97.1
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)
10.971.0265.60.391.722.09

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1B1Y0.9738.8552537101277994.5150.1140.1130.120.13040.13RANDOM8.6
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]
0.3250.078-0.403
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.115
r_sphericity_free19.168
r_dihedral_angle_4_deg14.432
r_dihedral_angle_3_deg11.689
r_sphericity_bonded6.725
r_scangle_it6.615
r_dihedral_angle_1_deg5.999
r_scbond_it5.159
r_mcangle_it3.742
r_rigid_bond_restr2.647
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.115
r_sphericity_free19.168
r_dihedral_angle_4_deg14.432
r_dihedral_angle_3_deg11.689
r_sphericity_bonded6.725
r_scangle_it6.615
r_dihedral_angle_1_deg5.999
r_scbond_it5.159
r_mcangle_it3.742
r_rigid_bond_restr2.647
r_mcbond_it2.549
r_angle_refined_deg1.565
r_mcbond_other1.362
r_symmetry_vdw_other0.24
r_chiral_restr0.095
r_bond_refined_d0.014
r_gen_planes_refined0.01
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3894
Nucleic Acid Atoms
Solvent Atoms948
Heterogen Atoms8

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing