9M0B | pdb_00009m0b

Crystal structure of alpha-agarase AGA from Catenovulum maritimum


X-RAY DIFFRACTION

Serial Crystallography (SX)

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelAlphaFold 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.8278Ammonium Sulfate, HEPES pH7.8, PEG8000
Crystal Properties
Matthews coefficientSolvent content
2.7955.87

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 129.242α = 90
b = 136.065β = 90
c = 109.173γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray278PIXELDECTRIS PILATUS 12M2024-12-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL02U10.979137SSRFBL02U1

Serial Crystallography

Sample delivery method
Diffraction IDDescriptionSample Delivery Method
1fixed target

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
11.64109.171000.0460.0480.0130.997913.7234458
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.641.761000.0470.0490.01310.713.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT1.64109.172223671163299.840.188760.18710.19190.220120.2208RANDOM22.255
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]
0.64-0.57-0.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg12.706
r_dihedral_angle_2_deg7.798
r_dihedral_angle_1_deg7.204
r_long_range_B_refined6.563
r_long_range_B_other6.447
r_scangle_other4.706
r_mcangle_it3.242
r_mcangle_other3.242
r_scbond_it3.111
r_scbond_other3.024
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg12.706
r_dihedral_angle_2_deg7.798
r_dihedral_angle_1_deg7.204
r_long_range_B_refined6.563
r_long_range_B_other6.447
r_scangle_other4.706
r_mcangle_it3.242
r_mcangle_other3.242
r_scbond_it3.111
r_scbond_other3.024
r_mcbond_it2.245
r_mcbond_other2.245
r_angle_refined_deg1.664
r_angle_other_deg0.594
r_chiral_restr0.087
r_bond_refined_d0.008
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
r_dihedral_angle_4_deg
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_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms12198
Nucleic Acid Atoms
Solvent Atoms1367
Heterogen Atoms162

Software

Software
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing