7V92

Crystal Structure of a thermostable mutant of the Catalytic Domain of GH19 Chitinase from Gazyumaru, Ficus microcarpa


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4TX7 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP529318% (w/v) Polyethylene glycol 20K, 0.1 M sodium citrate (pH 5.0), and 3% (v/v) Glycerol.
Crystal Properties
Matthews coefficientSolvent content
2.3247

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 140.579α = 90
b = 38.894β = 96.028
c = 177.739γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray95PIXELDECTRIS PILATUS 2M-F2017-11-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NE3A1.0Photon FactoryAR-NE3A

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
11.647.5896.60.998123.4799385
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)
11.61.70.922

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-VALUE4tx71.60747.58122333611797.280.2150.21370.243721.908
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]
-0.0160.0080.0080.006
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.518
r_dihedral_angle_3_deg13.242
r_dihedral_angle_4_deg12.623
r_dihedral_angle_1_deg6.166
r_lrange_it3.961
r_lrange_other3.859
r_scangle_it2.41
r_scangle_other2.41
r_mcangle_other2.136
r_mcangle_it2.135
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.518
r_dihedral_angle_3_deg13.242
r_dihedral_angle_4_deg12.623
r_dihedral_angle_1_deg6.166
r_lrange_it3.961
r_lrange_other3.859
r_scangle_it2.41
r_scangle_other2.41
r_mcangle_other2.136
r_mcangle_it2.135
r_scbond_it1.514
r_scbond_other1.511
r_angle_refined_deg1.356
r_angle_other_deg1.343
r_mcbond_it1.342
r_mcbond_other1.337
r_nbd_refined0.206
r_symmetry_nbd_other0.185
r_nbtor_refined0.177
r_symmetry_xyhbond_nbd_refined0.166
r_nbd_other0.158
r_xyhbond_nbd_refined0.141
r_symmetry_nbd_refined0.101
r_symmetry_nbtor_other0.078
r_chiral_restr0.07
r_bond_refined_d0.006
r_gen_planes_refined0.006
r_symmetry_xyhbond_nbd_other0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7541
Nucleic Acid Atoms
Solvent Atoms729
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata collection
XDSdata reduction
PHASERphasing