4AYP

Structure of The GH47 processing alpha-1,2-mannosidase from Caulobacter strain K31 in complex with thiomannobioside


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherPREVIOUSLY SOLVED NATIVE STRUCTURE

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.50.2 M AMMONIUM ACTETATE, 0.1 M BIS-TRIS PH 6.5, 22% WT/VOL PEG 3350
Crystal Properties
Matthews coefficientSolvent content
238.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 144.135α = 90
b = 144.135β = 90
c = 50.301γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MMIRRORS2011-07-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I03DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
10.8546.6597.20.0416.95.13332811.7
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
10.850.980.80.571.72.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPREVIOUSLY SOLVED NATIVE STRUCTURE0.8539.163164491682197.170.096920.096460.10555RANDOM8.802
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]
0.040.020.04-0.06
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free35.618
r_dihedral_angle_2_deg34.332
r_dihedral_angle_4_deg17.833
r_dihedral_angle_3_deg11.963
r_sphericity_bonded9.068
r_dihedral_angle_1_deg6.041
r_rigid_bond_restr2.031
r_angle_refined_deg1.427
r_angle_other_deg0.801
r_symmetry_hbond_refined0.616
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free35.618
r_dihedral_angle_2_deg34.332
r_dihedral_angle_4_deg17.833
r_dihedral_angle_3_deg11.963
r_sphericity_bonded9.068
r_dihedral_angle_1_deg6.041
r_rigid_bond_restr2.031
r_angle_refined_deg1.427
r_angle_other_deg0.801
r_symmetry_hbond_refined0.616
r_symmetry_vdw_refined0.321
r_nbd_refined0.282
r_symmetry_vdw_other0.235
r_nbtor_refined0.186
r_symmetry_hbond_other0.183
r_nbd_other0.168
r_xyhbond_nbd_refined0.114
r_nbtor_other0.085
r_chiral_restr0.082
r_metal_ion_refined0.068
r_bond_refined_d0.01
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3449
Nucleic Acid Atoms
Solvent Atoms781
Heterogen Atoms27

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing