4AYR

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4AYQPDB ENTRY 4AYQ

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
1.9938.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 143.919α = 90
b = 143.919β = 90
c = 50.186γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2MMIRRORS2012-03-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-1DiamondI04-1

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
11.146.5589.60.0432.29.11409452
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)
11.11.1649.50.216.74.2

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 REPLACEMENTTHROUGHOUTPDB ENTRY 4AYQ1.146.6133840710589.530.083620.082640.10208RANDOM9.843
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]
-0.05-0.03-0.050.08
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free36.735
r_dihedral_angle_2_deg33.099
r_dihedral_angle_4_deg16.668
r_dihedral_angle_3_deg12.157
r_sphericity_bonded7.229
r_dihedral_angle_1_deg6.001
r_rigid_bond_restr1.588
r_angle_refined_deg1.394
r_angle_other_deg0.816
r_symmetry_vdw_refined0.338
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free36.735
r_dihedral_angle_2_deg33.099
r_dihedral_angle_4_deg16.668
r_dihedral_angle_3_deg12.157
r_sphericity_bonded7.229
r_dihedral_angle_1_deg6.001
r_rigid_bond_restr1.588
r_angle_refined_deg1.394
r_angle_other_deg0.816
r_symmetry_vdw_refined0.338
r_symmetry_hbond_refined0.338
r_chiral_restr0.28
r_nbd_refined0.275
r_symmetry_vdw_other0.274
r_nbtor_refined0.188
r_nbd_other0.172
r_xyhbond_nbd_refined0.171
r_nbtor_other0.085
r_metal_ion_refined0.054
r_xyhbond_nbd_other0.019
r_bond_refined_d0.01
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
r_metal_ion_other
r_symmetry_hbond_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 Atoms3429
Nucleic Acid Atoms
Solvent Atoms724
Heterogen Atoms84

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing