6ZFQ

Structure of the catalytic domain of human endo-alpha-mannosidase MANEA in complex with bis-tris


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.5292100 mM bis-tris pH 5.5, 25% w/v PEG 3350. Protein at 10 mg/ml in 25 mM HEPES pH 7.0, 200 mM NaCl buffer with 2.23 mM GlcIFG and 2.23 mM alpha-1,2-mannobiose (10 x molar ratio). 300 nl droplet (150 nl protein solution, 150 nl reservoir solution). The ligand additives are probably not required for crystallization.
Crystal Properties
Matthews coefficientSolvent content
2.1141.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.812α = 90
b = 106.994β = 110.315
c = 43.884γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2018-07-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I240.97718DiamondI24

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
11.238.4199.40.0490.0570.0280.99910.63.811449812.49
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)
11.21.2294.70.6950.8540.4850.8041.52.8

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-VALUE6ZFN1.238.41114455555599.3080.1430.14090.181223.781
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]
-3.6121.62-0.7842.508
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.039
r_rigid_bond_restr16.007
r_dihedral_angle_4_deg14.289
r_dihedral_angle_3_deg12.655
r_dihedral_angle_1_deg6.338
r_lrange_it5.054
r_lrange_other4.832
r_scangle_it4.778
r_scangle_other4.777
r_scbond_it4.048
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.039
r_rigid_bond_restr16.007
r_dihedral_angle_4_deg14.289
r_dihedral_angle_3_deg12.655
r_dihedral_angle_1_deg6.338
r_lrange_it5.054
r_lrange_other4.832
r_scangle_it4.778
r_scangle_other4.777
r_scbond_it4.048
r_scbond_other4.047
r_mcangle_other3.811
r_mcangle_it3.759
r_mcbond_it3.271
r_mcbond_other3.233
r_angle_other_deg2.353
r_angle_refined_deg1.82
r_symmetry_xyhbond_nbd_other0.242
r_nbd_other0.22
r_nbd_refined0.218
r_symmetry_nbd_other0.212
r_symmetry_nbd_refined0.198
r_nbtor_refined0.189
r_xyhbond_nbd_refined0.159
r_symmetry_xyhbond_nbd_refined0.134
r_chiral_restr0.116
r_symmetry_nbtor_other0.089
r_bond_other_d0.034
r_gen_planes_other0.025
r_gen_planes_refined0.014
r_bond_refined_d0.013
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2865
Nucleic Acid Atoms
Solvent Atoms455
Heterogen Atoms14

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing