5NJF | pdb_00005njf

E. coli Microcin-processing metalloprotease TldD/E (TldD H262A mutant) with pentapeptide bound

X-RAY DIFFRACTION

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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
2.34	47.33

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.16	α = 90
b = 174.48	β = 90.04
c = 83.65	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	1.42	65.16	99	0.084	0.091	0.035	0.998	11.9	6.8		346357			15.3

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	1.42	1.46	98		1.543	1.677	0.647	0.44		6.5

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	5NJ5	1.42	65.16	328992	17364	98.82	0.1402	0.1386	0.1474	0.1711	0.1778	RANDOM	19.142

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]
-17.86		1.63	15.97		1.89

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.917
r_sphericity_free	25.334
r_dihedral_angle_4_deg	17.143
r_dihedral_angle_3_deg	12.246
r_sphericity_bonded	8.812
r_dihedral_angle_1_deg	6.054
r_rigid_bond_restr	1.497
r_angle_refined_deg	1.346
r_angle_other_deg	0.913
r_chiral_restr	0.082
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	13867
Nucleic Acid Atoms
Solvent Atoms	2073
Heterogen Atoms	114

Software

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