6ZDK

Structure of the catalytic domain of human endo-alpha-mannosidase MANEA in complex with HEPES and hexatungstotellurate(VI) TEW


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6ZDF 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5292100 mM HEPES pH 7.5, 200 mM MgCl2, 30% v/v PEG 400 (Alfa Aesar), 1 mM Anderson-Evans polyoxotungstate TEW. Protein at 10 mg/ml in 25 mM HEPES pH 7.0, 200 mM NaCl buffer.
Crystal Properties
Matthews coefficientSolvent content
2.6153.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 128.968α = 90
b = 128.968β = 90
c = 48.791γ = 120
Symmetry
Space GroupP 62

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2018-01-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.97625DiamondI03

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
1264.4899.60.1260.1490.0780.9926.23.531607
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)
122.0598.30.7390.8690.450.4111.53.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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-VALUE6ZDF264.4831481155499.5920.1980.19560.23532.842
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]
-1.779-0.89-1.7795.772
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.789
r_dihedral_angle_4_deg18.755
r_dihedral_angle_3_deg15.88
r_dihedral_angle_1_deg6.13
r_lrange_it5.317
r_lrange_other5.29
r_scangle_it4.459
r_scangle_other3.617
r_scbond_it3.245
r_mcangle_other2.798
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.789
r_dihedral_angle_4_deg18.755
r_dihedral_angle_3_deg15.88
r_dihedral_angle_1_deg6.13
r_lrange_it5.317
r_lrange_other5.29
r_scangle_it4.459
r_scangle_other3.617
r_scbond_it3.245
r_mcangle_other2.798
r_mcangle_it2.793
r_angle_other_deg2.318
r_scbond_other2.224
r_angle_refined_deg1.963
r_mcbond_it1.804
r_mcbond_other1.775
r_nbd_other0.266
r_symmetry_nbd_refined0.232
r_symmetry_nbd_other0.196
r_nbd_refined0.194
r_symmetry_xyhbond_nbd_refined0.185
r_nbtor_refined0.182
r_xyhbond_nbd_refined0.149
r_chiral_restr0.129
r_symmetry_nbtor_other0.077
r_bond_other_d0.035
r_metal_ion_refined0.035
r_symmetry_xyhbond_nbd_other0.033
r_bond_refined_d0.015
r_gen_planes_refined0.007
r_gen_planes_other0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2986
Nucleic Acid Atoms
Solvent Atoms165
Heterogen Atoms109

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing