8ZAZ | pdb_00008zaz

Crystal structure of Chitinase 3-like protein 1

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1HJX

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		298	10% PEG8000, 0.5 M NaCl, 0.1 M sodium citrate pH 3.5

Crystal Properties
Matthews coefficient	Solvent content
2.83	56.58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 109.48	α = 90
b = 122.39	β = 90
c = 137.11	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 6M		2023-06-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL18U1	0.97853	SSRF	BL18U1

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	2.31	50.84	100	0.167	12.2	13.4		81373

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.31	2.37			1.844

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.31	49.97	81297	3961	99.964	0.204	0.2013	0.207	0.2568	0.2612	51.425

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]
-1.866			-0.668		2.534

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.878
r_dihedral_angle_3_deg	13.339
r_lrange_other	13.237
r_lrange_it	13.236
r_dihedral_angle_2_deg	10.611
r_scangle_it	8.543
r_scangle_other	8.543
r_mcangle_it	7.623
r_mcangle_other	7.623
r_dihedral_angle_1_deg	7.338
r_scbond_it	5.591
r_scbond_other	5.591
r_mcbond_it	5.201
r_mcbond_other	5.201
r_angle_refined_deg	1.688
r_angle_other_deg	0.594
r_symmetry_xyhbond_nbd_refined	0.371
r_nbd_refined	0.233
r_symmetry_nbd_refined	0.221
r_xyhbond_nbd_refined	0.219
r_symmetry_nbd_other	0.199
r_nbtor_refined	0.189
r_nbd_other	0.179
r_xyhbond_nbd_other	0.092
r_symmetry_nbtor_other	0.082
r_chiral_restr	0.08
r_symmetry_xyhbond_nbd_other	0.029
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11412
Nucleic Acid Atoms
Solvent Atoms	252
Heterogen Atoms	60

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-2000	data scaling
MOLREP	phasing