6ZFN

Structure of an inactive E404Q variant of the catalytic domain of human endo-alpha-mannosidase MANEA in complex with 1-methyl alpha-1,2-mannobiose


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.6279100 mM sodium acetate pH 4.6, 200 mM ammonium sulfate, 12.8% PEG-MME 2000. Protein at 10 mg/ml in 25 mM HEPES pH 7.0, 200 mM NaCl buffer with 2.3 mM GlcMan4OMe (10 x molar ratio). 500 nl protein solution and 500 nl reservoir solution.
Crystal Properties
Matthews coefficientSolvent content
2.0740.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.752α = 90
b = 81.68β = 92.934
c = 52.994γ = 90
Symmetry
Space GroupP 1 21 1

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
11.152.9297.60.0540.0610.0290.99811.93.71432988.98
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)
11.11.1271.30.2230.2710.150.9443.32.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE6ZDF1.152.92143263722597.5290.1070.10630.127914.999
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]
-0.257-0.1730.472-0.196
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.659
r_dihedral_angle_3_deg12.836
r_dihedral_angle_4_deg11.791
r_rigid_bond_restr11.682
r_dihedral_angle_1_deg11.196
r_lrange_it3.474
r_lrange_other3.472
r_scangle_it2.554
r_scangle_other2.554
r_angle_other_deg2.503
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.659
r_dihedral_angle_3_deg12.836
r_dihedral_angle_4_deg11.791
r_rigid_bond_restr11.682
r_dihedral_angle_1_deg11.196
r_lrange_it3.474
r_lrange_other3.472
r_scangle_it2.554
r_scangle_other2.554
r_angle_other_deg2.503
r_mcangle_it2.319
r_mcangle_other2.318
r_angle_refined_deg2.077
r_scbond_it1.974
r_scbond_other1.974
r_mcbond_other1.705
r_mcbond_it1.704
r_symmetry_nbd_refined0.283
r_nbd_other0.236
r_nbd_refined0.234
r_symmetry_nbd_other0.207
r_nbtor_refined0.193
r_symmetry_xyhbond_nbd_refined0.172
r_chiral_restr0.158
r_xyhbond_nbd_refined0.158
r_symmetry_xyhbond_nbd_other0.087
r_symmetry_nbtor_other0.079
r_bond_other_d0.033
r_bond_refined_d0.018
r_gen_planes_other0.018
r_gen_planes_refined0.013
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2922
Nucleic Acid Atoms
Solvent Atoms478
Heterogen Atoms29

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing