3PW3 | pdb_00003pw3

Crystal structure of a cysteine protease (BDI_2249) from Parabacteroides distasonis ATCC 8503 at 2.23 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.2	293	20.00% polyethylene glycol 3350, 0.2000M potassium sodium tartrate, No Buffer pH 7.2, Additive: 0.001 M zinc chloride, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.03	59.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 104.592	α = 90
b = 137.81	β = 90
c = 223.165	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	CCD	MARMOSAIC 325 mm CCD	flat collimating Rh coated mirror, toroidal focussing mirror	2010-07-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL14-1		SSRL	BL14-1

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	29.966	98.7	0.073	13.23			154800		-3	38.695

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	2.23	2.31	99.6		0.534	2.6

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	2.23	29.966	154749	7771	98.36	0.1603	0.1592	0.16	0.1812	0.18	RANDOM	40.4993

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]
-0.61			0.23		0.39

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.573
r_dihedral_angle_4_deg	16.558
r_dihedral_angle_3_deg	14.189
r_dihedral_angle_1_deg	5.885
r_angle_refined_deg	1.237
r_angle_other_deg	1.109
r_chiral_restr	0.078
r_bond_refined_d	0.012
r_gen_planes_refined	0.007
r_bond_other_d	0.005

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.573
r_dihedral_angle_4_deg	16.558
r_dihedral_angle_3_deg	14.189
r_dihedral_angle_1_deg	5.885
r_angle_refined_deg	1.237
r_angle_other_deg	1.109
r_chiral_restr	0.078
r_bond_refined_d	0.012
r_gen_planes_refined	0.007
r_bond_other_d	0.005
r_gen_planes_other	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	17102
Nucleic Acid Atoms
Solvent Atoms	2003
Heterogen Atoms	87

Software

Software
Software Name	Purpose
SHELX	phasing
REFMAC	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing

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.