8RIC | pdb_00008ric

Crystallographic structure of oligosaccharide dehydrogenase from Pycnoporus cinnabarinus bound to Sinapic Acid, tetragonal crystal


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6XUU 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2942 M AMMONIUM SULFATE
Crystal Properties
Matthews coefficientSolvent content
2.8857.28

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 147.531α = 90
b = 147.531β = 90
c = 142.79γ = 90
Symmetry
Space GroupP 42 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 9M2021-09-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSOLEIL BEAMLINE PROXIMA 20.98011SOLEILPROXIMA 2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
11.8649.051000.0970.9968.427.6131815
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.861.891001.7890.3360.828.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)Mean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE1.8649.0413173466851000.1690.17210.2020.204626.62
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]
-0.006-0.0060.013
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg19.219
r_dihedral_angle_3_deg16.218
r_dihedral_angle_1_deg6.753
r_scangle_it4.514
r_scbond_it2.92
r_mcangle_it2.392
r_angle_refined_deg2.049
r_mcbond_it1.689
r_nbtor_refined0.304
r_xyhbond_nbd_refined0.21
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg19.219
r_dihedral_angle_3_deg16.218
r_dihedral_angle_1_deg6.753
r_scangle_it4.514
r_scbond_it2.92
r_mcangle_it2.392
r_angle_refined_deg2.049
r_mcbond_it1.689
r_nbtor_refined0.304
r_xyhbond_nbd_refined0.21
r_nbd_refined0.206
r_chiral_restr0.112
r_bond_refined_d0.015
r_gen_planes_refined0.015
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
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_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8820
Nucleic Acid Atoms
Solvent Atoms1146
Heterogen Atoms516

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing