6SH2 | pdb_00006sh2

Crystal structure of human neprilysin E584D in complex with C-type natriuretic peptide.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6GID

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		291.15	Potassium nitrate, Sodium iodide, PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.43	49.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 109.267	α = 90
b = 109.267	β = 90
c = 112.579	γ = 120

Symmetry
Space Group	P 32 2 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 EIGER2 X 16M		2019-05-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9762	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	2.6	72.44	100	1	17.3	39.9		24386

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.6	2.72			0.604

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	6GID	2.6	72.44	24353	1287	99.975	0.246	0.2435	0.24	0.2866	0.29	91.557

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]
1.816	0.908		1.816		-5.892

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.303
r_dihedral_angle_3_deg	14.359
r_dihedral_angle_4_deg	13.397
r_dihedral_angle_1_deg	4.852
r_lrange_it	4.753
r_lrange_other	4.752
r_mcangle_it	2.931
r_mcangle_other	2.931
r_scangle_it	2.567
r_scangle_other	2.567
r_mcbond_it	1.698
r_mcbond_other	1.697
r_scbond_it	1.418
r_scbond_other	1.418
r_angle_refined_deg	1.148
r_angle_other_deg	1.114
r_symmetry_nbd_other	0.162
r_nbd_refined	0.157
r_nbtor_refined	0.151
r_nbd_other	0.134
r_xyhbond_nbd_refined	0.1
r_metal_ion_refined	0.084
r_symmetry_nbtor_other	0.081
r_symmetry_nbd_refined	0.057
r_symmetry_xyhbond_nbd_refined	0.057
r_chiral_restr	0.031
r_bond_refined_d	0.002
r_bond_other_d	0.002
r_gen_planes_refined	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5475
Nucleic Acid Atoms
Solvent Atoms	1
Heterogen Atoms	59

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
Aimless	data scaling
PHASER	phasing