3ARP

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

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	48.68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.24	α = 90
b = 50.97	β = 99.53
c = 93.31	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		2009-04-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.97941	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	1.55	19.976	96.7	0.043	18.46			85182		-3	21.302

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	1.55	1.59	87		0.322	0.394	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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3b9a	1.55	19.976	85180	4259	100	0.1483	0.1463	0.187	RANDOM	16.8028

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]
0.16		0.42	0.03		-0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.387
r_dihedral_angle_4_deg	15.171
r_dihedral_angle_3_deg	12.491
r_dihedral_angle_1_deg	6.449
r_scangle_it	4.878
r_scbond_it	3.336
r_angle_refined_deg	2.391
r_mcangle_it	2.337
r_mcbond_it	1.468
r_chiral_restr	0.172

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.387
r_dihedral_angle_4_deg	15.171
r_dihedral_angle_3_deg	12.491
r_dihedral_angle_1_deg	6.449
r_scangle_it	4.878
r_scbond_it	3.336
r_angle_refined_deg	2.391
r_mcangle_it	2.337
r_mcbond_it	1.468
r_chiral_restr	0.172
r_bond_refined_d	0.029
r_gen_planes_refined	0.016

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4397
Nucleic Acid Atoms
Solvent Atoms	884
Heterogen Atoms	52

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.