6ZDC

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5M17 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6292100 mM MIB buffer, pH 6.0. Protein at 5.5 mg/ml in 50 mM potassium phosphate, 50 mM KCl. 150 nl protein solution and 150 nl reservoir solution.
Crystal Properties
Matthews coefficientSolvent content
2.5351.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 38.467α = 90
b = 86.535β = 90
c = 135.916γ = 90
Symmetry
Space GroupP 2 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2017-01-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.9763DiamondI03

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
12.25135.9298.10.20.210.0610.994711.42187640.95
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)
12.252.3384.51.8722.0290.750.3450.96.9

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-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT5M172.25173.10321817110697.7640.1790.17690.2234RANDOM47.23
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]
-0.734-2.6443.378
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.041
r_dihedral_angle_3_deg15.072
r_dihedral_angle_4_deg14.786
r_lrange_it8.161
r_lrange_other8.116
r_dihedral_angle_1_deg6.494
r_scangle_it5.529
r_scangle_other5.527
r_mcangle_it5.338
r_mcangle_other5.337
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.041
r_dihedral_angle_3_deg15.072
r_dihedral_angle_4_deg14.786
r_lrange_it8.161
r_lrange_other8.116
r_dihedral_angle_1_deg6.494
r_scangle_it5.529
r_scangle_other5.527
r_mcangle_it5.338
r_mcangle_other5.337
r_scbond_it3.47
r_scbond_other3.469
r_mcbond_it3.412
r_mcbond_other3.408
r_angle_other_deg2.341
r_angle_refined_deg1.889
r_nbd_other0.246
r_symmetry_nbd_refined0.208
r_nbd_refined0.202
r_symmetry_nbd_other0.201
r_nbtor_refined0.182
r_symmetry_xyhbond_nbd_refined0.176
r_xyhbond_nbd_refined0.141
r_chiral_restr0.134
r_symmetry_xyhbond_nbd_other0.112
r_symmetry_nbtor_other0.079
r_bond_other_d0.035
r_bond_refined_d0.015
r_gen_planes_other0.008
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2877
Nucleic Acid Atoms
Solvent Atoms183
Heterogen Atoms1

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing