5CER

Bd0816 Predatory Endopeptidase from Bdellovibrio bacteriovorus in complex with immunity protein Bd3460

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	298	0.1M Na HEPES pH 7.5, 0.2M MgCl2, 25% w/v PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.63	53.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 237.45	α = 90
b = 212.32	β = 90
c = 90.9	γ = 90

Symmetry
Space Group	P 21 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M-F		2014-09-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.92001	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	2.48	100	99	0.156	15.1	13.5		153169

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	5CEC	2.48	100	153169	7978	98.79	0.2167	0.215	0.2491	RANDOM	43.935

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]
2.18			-0.49		-1.69

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.435
r_dihedral_angle_3_deg	16.141
r_dihedral_angle_4_deg	13.982
r_dihedral_angle_1_deg	6.437
r_angle_other_deg	1.861
r_mcangle_it	1.819
r_angle_refined_deg	1.683
r_mcbond_it	1.117
r_mcbond_other	1.117
r_chiral_restr	0.098

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.435
r_dihedral_angle_3_deg	16.141
r_dihedral_angle_4_deg	13.982
r_dihedral_angle_1_deg	6.437
r_angle_other_deg	1.861
r_mcangle_it	1.819
r_angle_refined_deg	1.683
r_mcbond_it	1.117
r_mcbond_other	1.117
r_chiral_restr	0.098
r_bond_refined_d	0.014
r_bond_other_d	0.01
r_gen_planes_refined	0.009
r_gen_planes_other	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	27359
Nucleic Acid Atoms
Solvent Atoms	1356
Heterogen Atoms	4

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XSCALE	data scaling
PHASER	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 R01GM133198.