4AW7

BpGH86A: A beta-porphyranase of glycoside hydrolase family 86 from the human gut bacterium Bacteroides plebeius


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
127% PEG MME 2000, 0.1 M POTASSIUM THIOCYANATE AND 150 MM SODIUM IODIDE
Crystal Properties
Matthews coefficientSolvent content
2.856

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.33α = 90
b = 87.7β = 90
c = 114.45γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100 MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCLSI BEAMLINE 08ID-1CLSI08ID-1

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
11.3331.41990.0615.87.31631942

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 DIFFRACTIONSADTHROUGHOUTNONE1.3369.61154892818999.660.138130.137420.15157RANDOM11.553
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]
-0.320.270.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.769
r_dihedral_angle_4_deg15.774
r_dihedral_angle_3_deg11.044
r_dihedral_angle_1_deg6.31
r_scangle_it4.767
r_scbond_it3.439
r_mcangle_it2.531
r_mcbond_it1.644
r_angle_refined_deg1.632
r_rigid_bond_restr1.421
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.769
r_dihedral_angle_4_deg15.774
r_dihedral_angle_3_deg11.044
r_dihedral_angle_1_deg6.31
r_scangle_it4.767
r_scbond_it3.439
r_mcangle_it2.531
r_mcbond_it1.644
r_angle_refined_deg1.632
r_rigid_bond_restr1.421
r_angle_other_deg0.972
r_mcbond_other0.604
r_chiral_restr0.108
r_bond_refined_d0.015
r_gen_planes_refined0.009
r_bond_other_d0.002
r_gen_planes_other0.001
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4475
Nucleic Acid Atoms
Solvent Atoms594
Heterogen Atoms107

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling