3N13

Crystal stricture of D143A chitinase in complex with NAG from Bacillus cereus NCTU2


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3N12PDB ENTRY 3N12

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP629150mM potassium phosphate monobasic, 20%(w/v) PEG 8000, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.0339.28

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.717α = 90
b = 76.752β = 90
c = 78.502γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDADSC QUANTUM 3152009-11-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSRRC BEAMLINE BL13B11.00000NSRRCBL13B1

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
11.73099.90.0530.03624.13.733132
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)
1.71.7699.90.3570.363.63.63253

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 3N121.724.7731402167199.920.187930.186770.21022RANDOM16.18
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]
-0.78-0.261.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.743
r_dihedral_angle_4_deg12.764
r_dihedral_angle_3_deg11.929
r_dihedral_angle_1_deg5.239
r_scangle_it1.942
r_scbond_it1.22
r_angle_refined_deg0.984
r_mcangle_it0.718
r_mcbond_it0.371
r_chiral_restr0.067
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.743
r_dihedral_angle_4_deg12.764
r_dihedral_angle_3_deg11.929
r_dihedral_angle_1_deg5.239
r_scangle_it1.942
r_scbond_it1.22
r_angle_refined_deg0.984
r_mcangle_it0.718
r_mcbond_it0.371
r_chiral_restr0.067
r_bond_refined_d0.005
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2506
Nucleic Acid Atoms
Solvent Atoms146
Heterogen Atoms29

Software

Software
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling