5CEB

Bd3459 Predatory Endopeptidase from Bdellovibrio bacteriovorus, K38M form

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3V39

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		298	0.1M potassium thiocyanate, 30% w/v PEG 2000 MME

Crystal Properties
Matthews coefficient	Solvent content
2.43	49.29

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.93	α = 63.89
b = 65.04	β = 83.27
c = 73.816	γ = 83.2

Symmetry
Space Group	P 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	PIXEL	DECTRIS PILATUS 6M-F		2014-11-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.91739	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	1.93	100	85.7	0.036	16.2	3.8		56655

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	3v39	1.93	66.11	56655	2881	85.61	0.1976	0.1958	0.2322	RANDOM	44.292

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]
1.86	1.28	-0.85	0.56	-0.17	-1.62

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.398
r_dihedral_angle_4_deg	18.64
r_dihedral_angle_3_deg	13.898
r_dihedral_angle_1_deg	6.6
r_mcangle_it	3.579
r_mcbond_it	2.616
r_mcbond_other	2.615
r_angle_refined_deg	1.629
r_angle_other_deg	1.178
r_chiral_restr	0.103
r_bond_refined_d	0.016
r_gen_planes_refined	0.009
r_bond_other_d	0.005
r_gen_planes_other	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5971
Nucleic Acid Atoms
Solvent Atoms	300
Heterogen Atoms

Software

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