4QB6

Structure of CBM35 in complex with aldouronic acid


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4QB1 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP729320% PEG 6000, 0.2M Calcium chloride, 0.1M HEPES, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.7855.82

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 39.78α = 90
b = 47.35β = 90
c = 103.03γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray120PIXELDECTRIS PILATUS 6M-F2014-03-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.976250DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.3531.4851000.0840.02617.311.55028254365911
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.351.421000.4270.136.611.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4QB11.3551.5150282541390219299.960.165050.164390.17736RANDOM11.661
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]
0.650.17-0.82
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.577
r_dihedral_angle_4_deg15.884
r_dihedral_angle_3_deg11.064
r_dihedral_angle_1_deg7.032
r_long_range_B_refined4.138
r_long_range_B_other3.933
r_scangle_other2.277
r_mcangle_other1.703
r_mcangle_it1.694
r_angle_refined_deg1.577
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.577
r_dihedral_angle_4_deg15.884
r_dihedral_angle_3_deg11.064
r_dihedral_angle_1_deg7.032
r_long_range_B_refined4.138
r_long_range_B_other3.933
r_scangle_other2.277
r_mcangle_other1.703
r_mcangle_it1.694
r_angle_refined_deg1.577
r_scbond_it1.531
r_scbond_other1.53
r_mcbond_it1.03
r_mcbond_other1.002
r_angle_other_deg0.795
r_chiral_restr0.096
r_bond_refined_d0.014
r_gen_planes_refined0.008
r_gen_planes_other0.003
r_bond_other_d0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms980
Nucleic Acid Atoms
Solvent Atoms100
Heterogen Atoms23

Software

Software
Software NamePurpose
MOLREPphasing
REFMACrefinement
XDSdata reduction
SCALAdata scaling