3ART

Crystal Structure Analysis of Chitinase A from Vibrio harveyi with novel inhibitors - W275G mutant 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	5.5	293	26%(w/v) PEG 4000, 0.2M Ammonium Acetate, 0.1M Sodium Acetate, pH 5.5, hanging drop, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.6	α = 90
b = 84.15	β = 90
c = 102.6	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	IMAGE PLATE	MARRESEARCH	helios mirrors	2009-01-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	BRUKER AXS MICROSTAR	1.5418

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	2.23	19.936	98.3	0.082	17.64			28235		-3	23.618

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	2.23	2.29	84.3		0.39	0.447	4.6

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	2.23	19.936	28235	1412	100	0.1649	0.1616	0.2287	RANDOM	16.7136

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]
-0.01			-0.28		0.3

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.079
r_dihedral_angle_4_deg	18.693
r_dihedral_angle_3_deg	15.658
r_dihedral_angle_1_deg	6.666
r_scangle_it	4.333
r_scbond_it	2.917
r_angle_refined_deg	1.765
r_mcangle_it	1.671
r_mcbond_it	0.952
r_chiral_restr	0.128

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.079
r_dihedral_angle_4_deg	18.693
r_dihedral_angle_3_deg	15.658
r_dihedral_angle_1_deg	6.666
r_scangle_it	4.333
r_scbond_it	2.917
r_angle_refined_deg	1.765
r_mcangle_it	1.671
r_mcbond_it	0.952
r_chiral_restr	0.128
r_bond_refined_d	0.021
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4359
Nucleic Acid Atoms
Solvent Atoms	446
Heterogen Atoms	108

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.