1ITX

Catalytic Domain of Chitinase A1 from Bacillus circulans WL-12


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1CTNPDB ENTRY 1CTN

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.3293PEG 4000, potassium dihydrophosphate, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
1.9737.21

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.0073α = 109.2931
b = 46.8388β = 95.4547
c = 55.7001γ = 116.6796
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2001-05-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL41XU0.50000SPring-8BL41XU

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
11.136.79398.10.0420.04210.11.91398231398235.943
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)
11.11.1397.20.2480.2482.41.910242

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1CTN1.136.793139823139823712598.10.117350.117350.116280.13719RANDOM8.354
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_3_deg16.2
r_dihedral_angle_1_deg5.181
r_sphericity_free2.912
r_scangle_it2.764
r_sphericity_bonded2.237
r_scbond_it1.966
r_angle_refined_deg1.675
r_mcangle_it1.573
r_rigid_bond_restr1.17
r_nbtor_other1.137
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg16.2
r_dihedral_angle_1_deg5.181
r_sphericity_free2.912
r_scangle_it2.764
r_sphericity_bonded2.237
r_scbond_it1.966
r_angle_refined_deg1.675
r_mcangle_it1.573
r_rigid_bond_restr1.17
r_nbtor_other1.137
r_mcbond_it1.077
r_angle_other_deg0.864
r_nbd_refined0.831
r_nbd_other0.466
r_symmetry_vdw_other0.304
r_symmetry_vdw_refined0.293
r_xyhbond_nbd_refined0.17
r_symmetry_hbond_refined0.166
r_chiral_restr0.103
r_bond_refined_d0.012
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.002
r_symmetry_hbond_other
r_xyhbond_nbd_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3221
Nucleic Acid Atoms
Solvent Atoms770
Heterogen Atoms66

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
ARP/wARPmodel building
REFMACrefinement
CCP4data scaling