5NJC

E. coli Microcin-processing metalloprotease TldD/E (TldD E263A mutant) with hexapeptide bound

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5NJ5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	293	NULL

Crystal Properties
Matthews coefficient	Solvent content
2.36	47.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.29	α = 90
b = 175.44	β = 90.01
c = 84.33	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	PIXEL	DECTRIS PILATUS3 6M		2015-10-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.9282	Diamond	I04-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	1.35	65.29	97.7	0.067	0.073	0.028	0.999	17	6.9		403735			13.6

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.35	1.39	94.6		1.623	1.755	0.66	0.429		6.9

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	FOURIER SYNTHESIS	THROUGHOUT	5NJ5	1.35	65.29	383738	19995	97.64	0.1468	0.145	0.1828	RANDOM	16.998

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]
-18.18		0.52	13.3		4.88

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.969
r_sphericity_free	18.862
r_dihedral_angle_4_deg	15.524
r_dihedral_angle_3_deg	12.298
r_sphericity_bonded	8.629
r_dihedral_angle_1_deg	5.999
r_rigid_bond_restr	2.49
r_angle_refined_deg	1.38
r_angle_other_deg	0.929
r_chiral_restr	0.083

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.969
r_sphericity_free	18.862
r_dihedral_angle_4_deg	15.524
r_dihedral_angle_3_deg	12.298
r_sphericity_bonded	8.629
r_dihedral_angle_1_deg	5.999
r_rigid_bond_restr	2.49
r_angle_refined_deg	1.38
r_angle_other_deg	0.929
r_chiral_restr	0.083
r_bond_refined_d	0.01
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13906
Nucleic Acid Atoms
Solvent Atoms	2179
Heterogen Atoms	102

Software

Software
Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
REFMAC	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.