4CD7

The structure of GH113 beta-mannanase AaManA from Alicyclobacillus acidocaldarius in complex with ManIFG and beta-1,4-mannobiose


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3CIVPDB ENTRY 3CIV

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
14.60.1 M SODIUM ACETATE PH 4.6, 4% PEG 4000
Crystal Properties
Matthews coefficientSolvent content
2.5251

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 69.472α = 90
b = 76.586β = 90
c = 140.212γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MMIRRORS2013-05-26MSINGLE 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
11.6576.5997.90.166.76.3886672
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)
11.651.6878.30.631.84.7

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 3CIV1.6570.1183793446697.320.153130.150810.19617RANDOM15.621
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]
-0.40.6-0.2
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free30.61
r_dihedral_angle_2_deg28.686
r_dihedral_angle_4_deg15.523
r_dihedral_angle_3_deg12.606
r_sphericity_bonded8.839
r_dihedral_angle_1_deg6.118
r_scangle_it3.341
r_scbond_it2.773
r_rigid_bond_restr2.466
r_mcangle_it2.357
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free30.61
r_dihedral_angle_2_deg28.686
r_dihedral_angle_4_deg15.523
r_dihedral_angle_3_deg12.606
r_sphericity_bonded8.839
r_dihedral_angle_1_deg6.118
r_scangle_it3.341
r_scbond_it2.773
r_rigid_bond_restr2.466
r_mcangle_it2.357
r_mcbond_it1.975
r_mcbond_other1.975
r_angle_refined_deg1.405
r_angle_other_deg1.03
r_symmetry_vdw_refined0.344
r_nbd_refined0.244
r_symmetry_vdw_other0.192
r_nbtor_refined0.185
r_nbd_other0.176
r_xyhbond_nbd_refined0.125
r_chiral_restr0.106
r_xyhbond_nbd_other0.089
r_nbtor_other0.087
r_symmetry_hbond_refined0.073
r_bond_refined_d0.01
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4971
Nucleic Acid Atoms
Solvent Atoms470
Heterogen Atoms88

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing