3TI9

Crystal structure of the basic protease BprB from the ovine footrot pathogen, Dichelobacter nodosus

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6.5	293	PEG 1500, pH 6.5, vapor diffusion, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
1.94	36.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 38.462	α = 90
b = 90.514	β = 109.99
c = 44.06	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	IMAGE PLATE	RIGAKU RAXIS	mirrors	2007-06-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RUH3R	1.542

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.8	45.27				26267	24768

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.8	24.383	24768	1258	94.26	0.1591	0.1565	0.2067	RANDOM	12.461

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]
-0.22		0.03	0.25		-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.576
r_dihedral_angle_4_deg	16.28
r_dihedral_angle_3_deg	12.925
r_dihedral_angle_1_deg	5.466
r_scangle_it	3.709
r_scbond_it	2.6
r_mcangle_it	1.296
r_angle_refined_deg	1.054
r_mcbond_it	0.696
r_nbtor_refined	0.298

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.576
r_dihedral_angle_4_deg	16.28
r_dihedral_angle_3_deg	12.925
r_dihedral_angle_1_deg	5.466
r_scangle_it	3.709
r_scbond_it	2.6
r_mcangle_it	1.296
r_angle_refined_deg	1.054
r_mcbond_it	0.696
r_nbtor_refined	0.298
r_nbd_refined	0.195
r_symmetry_vdw_refined	0.155
r_symmetry_hbond_refined	0.108
r_xyhbond_nbd_refined	0.094
r_metal_ion_refined	0.081
r_chiral_restr	0.071
r_bond_refined_d	0.008
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2494
Nucleic Acid Atoms
Solvent Atoms	460
Heterogen Atoms	10

Software

Software
Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
MOSFLM	data reduction

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 R01GM133198.