6ZDL

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


X-RAY DIFFRACTION

Starting Model(s)

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

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
2.5852.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 127.864α = 90
b = 127.864β = 90
c = 48.809γ = 120
Symmetry
Space GroupP 62

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2018-02-05MSINGLE 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
11.931.971000.2030.2090.050.99810.517.63620830.3
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)
11.91.9499.83.433.5340.8430.546117.4

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-VALUE6ZDK1.931.9736184177999.890.1940.19270.223429.729
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]
-1.009-0.505-1.0093.273
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.506
r_dihedral_angle_4_deg16.361
r_dihedral_angle_3_deg14.233
r_dihedral_angle_1_deg6.008
r_lrange_it4.321
r_lrange_other4.299
r_scangle_it4.283
r_scangle_other4.283
r_scbond_it3.238
r_scbond_other3.238
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.506
r_dihedral_angle_4_deg16.361
r_dihedral_angle_3_deg14.233
r_dihedral_angle_1_deg6.008
r_lrange_it4.321
r_lrange_other4.299
r_scangle_it4.283
r_scangle_other4.283
r_scbond_it3.238
r_scbond_other3.238
r_angle_other_deg2.455
r_mcangle_it2.273
r_mcangle_other2.273
r_angle_refined_deg2.073
r_mcbond_it1.477
r_mcbond_other1.476
r_symmetry_nbd_refined0.348
r_nbd_other0.278
r_nbd_refined0.198
r_symmetry_nbd_other0.197
r_nbtor_refined0.178
r_chiral_restr0.133
r_xyhbond_nbd_refined0.128
r_symmetry_xyhbond_nbd_refined0.095
r_symmetry_nbtor_other0.08
r_bond_other_d0.035
r_bond_refined_d0.017
r_gen_planes_refined0.007
r_gen_planes_other0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2938
Nucleic Acid Atoms
Solvent Atoms113
Heterogen Atoms130

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
REFMACphasing