7ODJ

Exo-mannosidase from Cellvibrio mixtus bound to N-alkyl mannocyclophellitol aziridine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1UUQ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.62930.2 M ammonium sulfate, 24% PEG4000
Crystal Properties
Matthews coefficientSolvent content
2.3748.05

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 91.815α = 90
b = 102.23β = 90
c = 50.68γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 XE 16M2021-04-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.97629DiamondI03

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
11.368.40398.80.1160.1210.0350.99921.321.5116329
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)
11.31.3284.90.80.9980.5860.6314.8

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-VALUE1UUQ1.368.403116260581898.6360.1260.12460.157715.895
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]
-1.3990.9620.436
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.852
r_dihedral_angle_4_deg15.457
r_dihedral_angle_3_deg11.442
r_dihedral_angle_1_deg6.245
r_rigid_bond_restr4.168
r_scangle_it3.918
r_scangle_other3.917
r_lrange_it3.57
r_lrange_other3.436
r_scbond_it3.427
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.852
r_dihedral_angle_4_deg15.457
r_dihedral_angle_3_deg11.442
r_dihedral_angle_1_deg6.245
r_rigid_bond_restr4.168
r_scangle_it3.918
r_scangle_other3.917
r_lrange_it3.57
r_lrange_other3.436
r_scbond_it3.427
r_scbond_other3.426
r_mcangle_other2.301
r_mcangle_it2.293
r_mcbond_it2.075
r_angle_refined_deg1.917
r_mcbond_other1.848
r_angle_other_deg1.623
r_nbd_other0.265
r_symmetry_nbd_refined0.226
r_nbd_refined0.224
r_nbtor_refined0.189
r_symmetry_nbd_other0.184
r_xyhbond_nbd_refined0.144
r_chiral_restr0.117
r_symmetry_xyhbond_nbd_refined0.089
r_symmetry_nbtor_other0.088
r_chiral_restr_other0.075
r_bond_refined_d0.015
r_gen_planes_refined0.012
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3292
Nucleic Acid Atoms
Solvent Atoms424
Heterogen Atoms44

Software

Software
Software NamePurpose
REFMACrefinement
REFMACrefinement
Aimlessdata scaling
MOLREPphasing
Cootmodel building
REFMACrefinement
XDSdata reduction