3WZ1

Catalytic domain of beta-agarase from Microbulbifer thermotolerans JAMB-A94


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4ATF 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52831M trisodium citrate, 0.3M ammonium nitrtate, 3% ethanol, 100mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 283K
Crystal Properties
Matthews coefficientSolvent content
2.4349.36

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.624α = 90
b = 69.394β = 90
c = 90.367γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210r2012-05-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NW12A1.0Photon FactoryAR-NW12A

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
11.6501000.03159.57.241972
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)
11.61.661000.12418.37.1

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4ATF1.637.8639772211799.930.152560.151910.16463RANDOM12.759
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]
-0.010.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.976
r_dihedral_angle_4_deg15.23
r_dihedral_angle_3_deg11.25
r_dihedral_angle_1_deg7.672
r_long_range_B_refined3.687
r_angle_other_deg3.63
r_long_range_B_other3.318
r_scangle_other1.6
r_angle_refined_deg1.462
r_mcangle_it1.191
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.976
r_dihedral_angle_4_deg15.23
r_dihedral_angle_3_deg11.25
r_dihedral_angle_1_deg7.672
r_long_range_B_refined3.687
r_angle_other_deg3.63
r_long_range_B_other3.318
r_scangle_other1.6
r_angle_refined_deg1.462
r_mcangle_it1.191
r_mcangle_other1.19
r_scbond_it1.04
r_scbond_other1.038
r_mcbond_it0.722
r_mcbond_other0.717
r_chiral_restr0.084
r_gen_planes_other0.011
r_bond_refined_d0.009
r_gen_planes_refined0.007
r_bond_other_d
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2236
Nucleic Acid Atoms
Solvent Atoms260
Heterogen Atoms14

Software

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