8R70

Polysaccharide lyase BtPL33HA (BT4410) Y291A with HA dp4


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherUnpublished structure

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29520 % PEG 6000 0.1 M MES 0.1 M Ammonium chloride 20 mg/ml
Crystal Properties
Matthews coefficientSolvent content
2.652.69

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.64α = 90
b = 137.301β = 90
c = 202.842γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2022-07-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.95373DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.797113.70295.40.999146.8122182
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.7971.8930.6981.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE1.797113.702122182614987.050.1830.18060.223434.44
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]
-0.5320.0270.505
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg15.582
r_dihedral_angle_3_deg15.185
r_dihedral_angle_2_deg10.909
r_lrange_it7.143
r_lrange_other7.118
r_dihedral_angle_1_deg6.979
r_scangle_it5.708
r_scangle_other5.708
r_scbond_it4.084
r_scbond_other4.083
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg15.582
r_dihedral_angle_3_deg15.185
r_dihedral_angle_2_deg10.909
r_lrange_it7.143
r_lrange_other7.118
r_dihedral_angle_1_deg6.979
r_scangle_it5.708
r_scangle_other5.708
r_scbond_it4.084
r_scbond_other4.083
r_mcangle_it3.497
r_mcangle_other3.497
r_mcbond_it2.748
r_mcbond_other2.747
r_angle_refined_deg2.215
r_angle_other_deg0.755
r_nbd_other0.254
r_nbd_refined0.229
r_symmetry_xyhbond_nbd_refined0.212
r_symmetry_nbd_other0.196
r_nbtor_refined0.189
r_symmetry_nbd_refined0.182
r_xyhbond_nbd_refined0.168
r_chiral_restr0.113
r_symmetry_nbtor_other0.087
r_metal_ion_refined0.08
r_symmetry_xyhbond_nbd_other0.063
r_bond_refined_d0.014
r_gen_planes_refined0.012
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9855
Nucleic Acid Atoms
Solvent Atoms700
Heterogen Atoms129

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
STARANISOdata scaling
MOLREPphasing