3QOK

Crystal structure of putative chitinase II from Klebsiella pneumoniae


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.22890.2 M NaCl, 0.1 M Na2HPO4/KH2PO4, 10% PEG8K, pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
358.95

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 92.341α = 90
b = 110.672β = 90
c = 108.481γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rMIRRORS2010-10-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-IDAPS19-ID

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
12.65099.90.12514.75.517383-3
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)
2.62.6499.70.6332.14.7

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 DIFFRACTIONMR-SADTHROUGHOUT1ITX2.649.29172881728787299.410.181080.179460.21163RANDOM36.706
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]
-1.650.840.81
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.894
r_dihedral_angle_4_deg18.799
r_dihedral_angle_3_deg15.425
r_dihedral_angle_1_deg5.724
r_scangle_it2.789
r_scbond_it1.74
r_angle_refined_deg1.357
r_mcangle_it0.967
r_angle_other_deg0.897
r_mcbond_it0.489
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.894
r_dihedral_angle_4_deg18.799
r_dihedral_angle_3_deg15.425
r_dihedral_angle_1_deg5.724
r_scangle_it2.789
r_scbond_it1.74
r_angle_refined_deg1.357
r_mcangle_it0.967
r_angle_other_deg0.897
r_mcbond_it0.489
r_mcbond_other0.094
r_chiral_restr0.076
r_bond_refined_d0.013
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3059
Nucleic Acid Atoms
Solvent Atoms25
Heterogen Atoms18

Software

Software
Software NamePurpose
REFMACrefinement
Auto-Rickshawphasing
CNSrefinement
SBC-Collectdata collection
PHASERphasing
MLPHAREphasing
piratephasing
SHELXEmodel building
RESOLVEmodel building
BUCCANEERmodel building
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
CNSphasing
REFMACphasing
RESOLVEphasing
BUCCANEERphasing