6ZJ1

Structure of an inactive E404Q variant of the catalytic domain of human endo-alpha-mannosidase MANEA in complex with tetrasaccharide N-glycan fragment and hexatungstotellurate(VI) TEW


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP292100 mM HEPES pH 7.5 - 8.1, 200 mM MgCl2, 25-27.5% v/v PEG 400, 1 mM TEW Protein in 25 mM HEPES pH 7.0, 200 mM NaCl buffer at 10 mg/ml.
Crystal Properties
Matthews coefficientSolvent content
2.7154.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 129.414α = 90
b = 129.414β = 90
c = 50.201γ = 120
Symmetry
Space GroupP 62

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 XE 16M2019-03-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.95004DiamondI04

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
11.957112.07650.10.0930.0980.0290.99915.711.717490
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)
11.9572.15511.91.4481.5220.4630.6581.610.5

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-VALUE6ZFA1.95764.7071748884450.1220.1870.18380.252440.367
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]
-0.063-0.032-0.0630.205
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.769
r_dihedral_angle_3_deg15.956
r_dihedral_angle_4_deg13.486
r_dihedral_angle_1_deg7.275
r_lrange_it7.177
r_lrange_other7.166
r_scangle_it5.298
r_scangle_other5.297
r_mcangle_other4.767
r_mcangle_it4.758
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.769
r_dihedral_angle_3_deg15.956
r_dihedral_angle_4_deg13.486
r_dihedral_angle_1_deg7.275
r_lrange_it7.177
r_lrange_other7.166
r_scangle_it5.298
r_scangle_other5.297
r_mcangle_other4.767
r_mcangle_it4.758
r_scbond_it3.839
r_scbond_other3.839
r_mcbond_it3.259
r_mcbond_other3.229
r_angle_refined_deg1.76
r_angle_other_deg1.211
r_symmetry_xyhbond_nbd_refined0.321
r_nbd_other0.209
r_nbd_refined0.207
r_symmetry_nbd_other0.193
r_xyhbond_nbd_refined0.184
r_symmetry_nbd_refined0.18
r_nbtor_refined0.176
r_symmetry_nbtor_other0.081
r_chiral_restr0.074
r_symmetry_xyhbond_nbd_other0.016
r_bond_refined_d0.009
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2992
Nucleic Acid Atoms
Solvent Atoms133
Heterogen Atoms109

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
STARANISOdata processing
REFMACphasing
XDSdata reduction