3ARX | pdb_00003arx

Crystal Structure Analysis of Chitinase A from Vibrio harveyi with novel inhibitors - complex structure with Propentofylline

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3B9A

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	hanging drop	5.6	293	16%(W/V) PEG 4000, 21%(v/v) propanol, 0.1M Na-Acetate, pH 5.6, hanging drop, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.4	49.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.11	α = 90
b = 50.93	β = 99.45
c = 93.17	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MARMOSAIC 225 mm CCD		2009-07-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.97935	SLS	X10SA

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	1.16	40.656	98.4	0.059	12.52			204668		-3	15.495

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.16	1.19	88.1		0.285	0.363	3.3

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3b9a	1.16	40.656	204667	10234	98.43	0.1619	0.1606	0.16	0.1852	0.18	RANDOM	17.4306

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]
0.03		0.07	0.35		-0.36

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.519
r_dihedral_angle_4_deg	19.96
r_dihedral_angle_3_deg	11.79
r_dihedral_angle_1_deg	6.507
r_angle_refined_deg	2.597
r_chiral_restr	0.155
r_bond_refined_d	0.034
r_gen_planes_refined	0.017

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4405
Nucleic Acid Atoms
Solvent Atoms	1099
Heterogen Atoms	50

Software

Software
Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.