6SH1 | pdb_00006sh1

Crystal structure of substrate-free human neprilysin E584D.

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 bromide, Bis-Tris propane, PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.42

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 76.14	α = 90
b = 99.745	β = 106.231
c = 100.119	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 EIGER2 X 16M		2019-01-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9795	Diamond	I04

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	2.1	69.22	99.9	0.992	6.6	6.9		576297

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	2.1	2.14			0.464	1

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	2.1	69.22	83801	4268	99.917	0.221	0.2184	0.22	0.2614	0.27	40.443

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]
-1.422		-2.141	2.931		-0.224

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.974
r_dihedral_angle_4_deg	14.686
r_dihedral_angle_3_deg	14.516
r_dihedral_angle_1_deg	5.633
r_lrange_it	4.611
r_lrange_other	4.584
r_scangle_it	2.96
r_scangle_other	2.96
r_mcangle_it	2.586
r_mcangle_other	2.586
r_angle_other_deg	2.349
r_scbond_it	1.749
r_scbond_other	1.749
r_mcbond_it	1.583
r_mcbond_other	1.583
r_angle_refined_deg	1.212
r_symmetry_nbd_other	0.202
r_nbd_other	0.18
r_nbd_refined	0.175
r_nbtor_refined	0.154
r_xyhbond_nbd_refined	0.15
r_symmetry_xyhbond_nbd_refined	0.134
r_symmetry_nbd_refined	0.119
r_metal_ion_refined	0.106
r_symmetry_nbtor_other	0.057
r_chiral_restr	0.045
r_symmetry_xyhbond_nbd_other	0.037
r_bond_other_d	0.036
r_gen_planes_other	0.004
r_bond_refined_d	0.003
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11031
Nucleic Acid Atoms
Solvent Atoms	495
Heterogen Atoms	126

Software

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