6ZFA

Structure of the catalytic domain of human endo-alpha-mannosidase MANEA in complex with GlcIFG, alpha-1,2-mannobiose 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
2.5551.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 127.891α = 90
b = 127.891β = 90
c = 48.352γ = 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 I030.97622DiamondI03

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
11.8110.761000.1480.1530.0380.99913.416.54214921.59
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)
11.81.841000.9390.9690.2370.7822.916.6

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-VALUE6ZDK1.8110.75742104209499.9360.1870.18550.216624.343
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]
-0.893-0.447-0.8932.898
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.832
r_dihedral_angle_1_deg19.834
r_dihedral_angle_4_deg18.142
r_dihedral_angle_3_deg13.767
r_lrange_it5.036
r_lrange_other5.018
r_scangle_it4.06
r_scangle_other4.059
r_scbond_it3.09
r_scbond_other3.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.832
r_dihedral_angle_1_deg19.834
r_dihedral_angle_4_deg18.142
r_dihedral_angle_3_deg13.767
r_lrange_it5.036
r_lrange_other5.018
r_scangle_it4.06
r_scangle_other4.059
r_scbond_it3.09
r_scbond_other3.09
r_angle_other_deg2.732
r_mcangle_it2.291
r_mcangle_other2.291
r_angle_refined_deg2.215
r_mcbond_it1.519
r_mcbond_other1.518
r_symmetry_nbd_refined0.356
r_nbd_other0.268
r_symmetry_nbd_other0.204
r_nbd_refined0.197
r_nbtor_refined0.18
r_symmetry_xyhbond_nbd_refined0.142
r_chiral_restr0.137
r_xyhbond_nbd_refined0.135
r_symmetry_nbtor_other0.092
r_bond_other_d0.034
r_bond_refined_d0.017
r_gen_planes_refined0.011
r_gen_planes_other0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2942
Nucleic Acid Atoms
Solvent Atoms136
Heterogen Atoms153

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
REFMACphasing