4CD8

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


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
2.0640

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.82α = 90
b = 75.89β = 90
c = 91.48γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MMIRRORS2012-09-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I02DiamondI02

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
11.4758.4199.70.06146.3521762
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)
11.471.51990.712.66.2

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 3CIV1.4758.4149455265999.670.172740.170430.21511RANDOM21.867
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]
3.04-3.580.55
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.384
r_rigid_bond_restr27.306
r_sphericity_free23.15
r_sphericity_bonded15.67
r_dihedral_angle_4_deg13.583
r_dihedral_angle_3_deg12.195
r_dihedral_angle_1_deg6.41
r_scangle_it4.262
r_scbond_it3.962
r_mcangle_it3.423
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.384
r_rigid_bond_restr27.306
r_sphericity_free23.15
r_sphericity_bonded15.67
r_dihedral_angle_4_deg13.583
r_dihedral_angle_3_deg12.195
r_dihedral_angle_1_deg6.41
r_scangle_it4.262
r_scbond_it3.962
r_mcangle_it3.423
r_mcbond_it2.972
r_mcbond_other2.958
r_angle_refined_deg1.508
r_angle_other_deg0.834
r_symmetry_vdw_refined0.297
r_symmetry_vdw_other0.264
r_nbd_refined0.24
r_symmetry_hbond_refined0.2
r_nbtor_refined0.192
r_nbd_other0.176
r_xyhbond_nbd_refined0.116
r_chiral_restr0.09
r_nbtor_other0.083
r_xyhbond_nbd_other0.06
r_bond_refined_d0.013
r_gen_planes_refined0.008
r_gen_planes_other0.002
r_bond_other_d0.001
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 Atoms2453
Nucleic Acid Atoms
Solvent Atoms193
Heterogen Atoms25

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
MOLREPphasing