8BGP

N,N-diacetylchitobiose deacetylase from Pyrococcus chitonophagus anomalous data


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 8BGN 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP3082.0M ammonium sulfate, 0.1M HEPES pH 7.5, 2% v/v PEG 400
Crystal Properties
Matthews coefficientSolvent content
2.6653.77

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.642α = 90
b = 158.654β = 90
c = 158.517γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2021-07-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)1.2815PETRA III, EMBL c/o DESYP13 (MX1)

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
12.50645.797.30.19911.05212.98129806
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)
12.5062.6190.4318

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT8BGN2.5145.742432114563.210.21940.21830.2614RANDOM40.197
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]
-1.12.42-1.32
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.588
r_dihedral_angle_3_deg15.835
r_dihedral_angle_4_deg15.566
r_dihedral_angle_1_deg6.72
r_angle_refined_deg1.449
r_angle_other_deg1.191
r_chiral_restr0.064
r_bond_refined_d0.007
r_gen_planes_refined0.006
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.588
r_dihedral_angle_3_deg15.835
r_dihedral_angle_4_deg15.566
r_dihedral_angle_1_deg6.72
r_angle_refined_deg1.449
r_angle_other_deg1.191
r_chiral_restr0.064
r_bond_refined_d0.007
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms13088
Nucleic Acid Atoms
Solvent Atoms17
Heterogen Atoms12

Software

Software
Software NamePurpose
XSCALEdata scaling
XDSdata reduction
Cootmodel building
PHASERphasing
REFMACrefinement