6RZD

Crystal structure of an inverting family GH156 exosialidase from uncultured bacterium pG7


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherUnpublished SeMet derivative

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP62730.8 M sodium formate, 15% PEG 4000, 0.1 M sodium acetate
Crystal Properties
Matthews coefficientSolvent content
2.4249.11

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.112α = 90
b = 79.273β = 94.72
c = 112.214γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2018-05-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.9795DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
1264.671000.1980.2190.0940.9855.85.475801
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.0499.70.8090.8940.3770.5935.6

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 REPLACEMENTTHROUGHOUTUnpublished SeMet derivative264.6771915383999.930.23630.23370.2856RANDOM23.225
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]
0.38-0.89-0.09-0.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.417
r_dihedral_angle_4_deg20.078
r_dihedral_angle_3_deg14.723
r_dihedral_angle_1_deg7.756
r_angle_refined_deg1.855
r_angle_other_deg1.312
r_chiral_restr0.082
r_bond_refined_d0.012
r_gen_planes_refined0.01
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.417
r_dihedral_angle_4_deg20.078
r_dihedral_angle_3_deg14.723
r_dihedral_angle_1_deg7.756
r_angle_refined_deg1.855
r_angle_other_deg1.312
r_chiral_restr0.082
r_bond_refined_d0.012
r_gen_planes_refined0.01
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8020
Nucleic Acid Atoms
Solvent Atoms420
Heterogen Atoms106

Software

Software
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
Aimlessdata scaling
PHASERphasing
DIALSdata reduction