7NWO

A carbohydrate binding module family 9 (CBM9) from Caldicellulosiruptor kristjanssonii in complex with glucose


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1I8U 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.22930.1 M phosphate-citrate and 40% polyethylene glycol 300
Crystal Properties
Matthews coefficientSolvent content
4.3571.71

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 172.61α = 90
b = 172.61β = 90
c = 172.61γ = 90
Symmetry
Space GroupI 4 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2019-10-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)1.000000PETRA III, EMBL c/o DESYP13 (MX1)

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)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
12.749.87899.950.99917.1121.712395
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.72.7970.343

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE1i8u2.749.8312391124099.960.2640.25610.334289.965
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.903
r_dihedral_angle_3_deg16.64
r_lrange_it14.04
r_dihedral_angle_4_deg11.639
r_mcangle_it8.376
r_scangle_it7.602
r_dihedral_angle_1_deg7.045
r_mcbond_it5.26
r_scbond_it5.1
r_angle_refined_deg1.046
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.903
r_dihedral_angle_3_deg16.64
r_lrange_it14.04
r_dihedral_angle_4_deg11.639
r_mcangle_it8.376
r_scangle_it7.602
r_dihedral_angle_1_deg7.045
r_mcbond_it5.26
r_scbond_it5.1
r_angle_refined_deg1.046
r_nbtor_refined0.315
r_symmetry_xyhbond_nbd_refined0.253
r_symmetry_nbd_refined0.245
r_nbd_refined0.228
r_metal_ion_refined0.216
r_xyhbond_nbd_refined0.176
r_chiral_restr0.079
r_gen_planes_refined0.004
r_bond_refined_d0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1549
Nucleic Acid Atoms
Solvent Atoms100
Heterogen Atoms104

Software

Software
Software NamePurpose
REFMACrefinement
PHENIXphasing