8RIE | pdb_00008rie

Crystallographic structure of oligosaccharide dehydrogenase from Pycnoporus cinnabarinus bound to Guaiacol, 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 = 48.891α = 90
b = 61.53β = 90
c = 195.206γ = 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
11.29197.6294.50.0810.99713.412.657542
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)
11.2911.4261.3640.5871.6

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 REPLACEMENTTHROUGHOUT1.7897.6254200284399.130.170030.167510.17340.218640.2206RANDOM32.536
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]
-2.390.911.48
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.182
r_dihedral_angle_4_deg21.423
r_dihedral_angle_3_deg15.502
r_rigid_bond_restr8.462
r_dihedral_angle_1_deg7.489
r_long_range_B_refined2.25
r_angle_refined_deg1.69
r_long_range_B_other1.493
r_angle_other_deg1.387
r_scangle_other1.302
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.182
r_dihedral_angle_4_deg21.423
r_dihedral_angle_3_deg15.502
r_rigid_bond_restr8.462
r_dihedral_angle_1_deg7.489
r_long_range_B_refined2.25
r_angle_refined_deg1.69
r_long_range_B_other1.493
r_angle_other_deg1.387
r_scangle_other1.302
r_scbond_it1.078
r_scbond_other1.078
r_mcangle_other0.877
r_mcangle_it0.876
r_mcbond_it0.586
r_mcbond_other0.585
r_chiral_restr0.085
r_bond_refined_d0.012
r_gen_planes_refined0.01
r_bond_other_d0.004
r_gen_planes_other0.003
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 Atoms569
Heterogen Atoms188

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
STARANISOdata scaling
MOLREPphasing