4CD6

The structure of GH113 beta-mannanase AaManA from Alicyclobacillus acidocaldarius in complex with ManIFG


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
2.1743

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.92α = 90
b = 76.16β = 90
c = 93.73γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MMIRRORS2013-04-19MSINGLE 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
11.6446.8799.40.0712.76.3397382
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)
11.641.6999.10.612.55.7

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 3CIV1.6446.8737678199599.340.146510.143450.20828RANDOM32.018
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]
2.9-4.021.12
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free34.347
r_dihedral_angle_2_deg30.972
r_dihedral_angle_4_deg18.589
r_sphericity_bonded17.397
r_dihedral_angle_3_deg13.514
r_dihedral_angle_1_deg5.816
r_scangle_it5.423
r_mcangle_it4.513
r_scbond_it4.491
r_mcbond_it3.875
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free34.347
r_dihedral_angle_2_deg30.972
r_dihedral_angle_4_deg18.589
r_sphericity_bonded17.397
r_dihedral_angle_3_deg13.514
r_dihedral_angle_1_deg5.816
r_scangle_it5.423
r_mcangle_it4.513
r_scbond_it4.491
r_mcbond_it3.875
r_mcbond_other3.873
r_rigid_bond_restr3.285
r_angle_refined_deg1.363
r_angle_other_deg0.823
r_symmetry_vdw_refined0.3
r_symmetry_vdw_other0.251
r_nbd_refined0.246
r_nbtor_refined0.188
r_nbd_other0.181
r_xyhbond_nbd_refined0.133
r_chiral_restr0.084
r_nbtor_other0.083
r_symmetry_hbond_refined0.023
r_bond_refined_d0.011
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
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 Atoms2466
Nucleic Acid Atoms
Solvent Atoms189
Heterogen Atoms21

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing