7V91

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

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4TX7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	293	3% (w/v) gamma-polyglutamic acid low molecule, 25%(w/v) 2-Methy-2, 4-pentanediol, 0.1 M HEPES (pH 7.5), 0.5 M Ammonium sulfate

Crystal Properties
Matthews coefficient	Solvent content
2.44	49.56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.9	α = 90
b = 106.583	β = 90
c = 107.656	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS3 S 6M		2017-11-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-5A	1.0	Photon Factory	BL-5A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.6	50	99.8	0.061	46	7.3		1000279

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.6	1.63			0.381	0.937

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	4TX7	1.6	48.094	136887	6845	99.169	0.228	0.2269	0.2528	20.106

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]
0.001			0.001		-0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.566
r_dihedral_angle_3_deg	13.879
r_dihedral_angle_4_deg	11.608
r_dihedral_angle_1_deg	6.112
r_lrange_it	3.507
r_lrange_other	3.507
r_scangle_it	2.122
r_scangle_other	2.121
r_mcangle_it	1.881
r_mcangle_other	1.881
r_scbond_it	1.419
r_scbond_other	1.419
r_angle_refined_deg	1.4
r_angle_other_deg	1.394
r_mcbond_it	1.248
r_mcbond_other	1.246
r_nbd_refined	0.208
r_symmetry_nbd_other	0.187
r_nbd_other	0.181
r_nbtor_refined	0.178
r_symmetry_xyhbond_nbd_refined	0.154
r_symmetry_nbd_refined	0.15
r_xyhbond_nbd_refined	0.138
r_symmetry_nbtor_other	0.08
r_chiral_restr	0.07
r_symmetry_xyhbond_nbd_other	0.056
r_bond_refined_d	0.006
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7495
Nucleic Acid Atoms
Solvent Atoms	604
Heterogen Atoms	145

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing