8RID | pdb_00008rid

Crystallographic structure of oligosaccharide dehydrogenase from Pycnoporus cinnabarinus bound to Sinapic Acid, orthorhombic 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
2.3748.12

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.06α = 90
b = 61.883β = 90
c = 195.597γ = 90
Symmetry
Space GroupP 21 21 21

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)R Merge I (Observed)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
11.1997.9995.60.0760.9991412.8129361
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.191.2971.1190.7021.7

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 REPLACEMENTTHROUGHOUT1.397.99116481605483.210.14430.142510.14520.178240.1804RANDOM28.177
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]
1.3-2.461.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.592
r_dihedral_angle_4_deg18.506
r_dihedral_angle_3_deg14.802
r_dihedral_angle_1_deg7.247
r_rigid_bond_restr7.104
r_long_range_B_refined3.353
r_long_range_B_other3.128
r_scangle_other2.15
r_angle_refined_deg1.746
r_scbond_it1.716
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.592
r_dihedral_angle_4_deg18.506
r_dihedral_angle_3_deg14.802
r_dihedral_angle_1_deg7.247
r_rigid_bond_restr7.104
r_long_range_B_refined3.353
r_long_range_B_other3.128
r_scangle_other2.15
r_angle_refined_deg1.746
r_scbond_it1.716
r_scbond_other1.715
r_mcangle_other1.587
r_mcangle_it1.586
r_angle_other_deg1.486
r_mcbond_it1.18
r_mcbond_other1.167
r_chiral_restr0.096
r_bond_refined_d0.012
r_gen_planes_refined0.011
r_bond_other_d0.006
r_gen_planes_other0.002
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_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4410
Nucleic Acid Atoms
Solvent Atoms665
Heterogen Atoms193

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
STARANISOdata scaling
MOLREPphasing