9GBM | pdb_00009gbm

Human Angiotensin-1 converting enzyme C-domain in complex with a diprolyl inhibitor- SG3

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6F9T

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		289.15	0.1 M MIB pH 4.0, 5% glycerol, and 15% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.34	47.44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.886	α = 90
b = 84.131	β = 90
c = 132.664	γ = 90

Symmetry
Space Group	P 21 21 21

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 XE 16M		2019-09-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9159	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.9	132.66	100	0.057	0.996	8.5	12.2		50194

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	1.94			0.503	0.579	1.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	1.9	71.149	50106	2395	99.968	0.17	0.1678	0.1697	0.217	0.2197	27.778

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]
-1.157			1.643		-0.486

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.107
r_dihedral_angle_3_deg	14.731
r_dihedral_angle_2_deg	8.516
r_lrange_it	8.172
r_scangle_it	7.796
r_dihedral_angle_1_deg	6.276
r_scbond_it	5.448
r_mcangle_it	3.892
r_mcbond_it	3.067
r_angle_refined_deg	2.532

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.107
r_dihedral_angle_3_deg	14.731
r_dihedral_angle_2_deg	8.516
r_lrange_it	8.172
r_scangle_it	7.796
r_dihedral_angle_1_deg	6.276
r_scbond_it	5.448
r_mcangle_it	3.892
r_mcbond_it	3.067
r_angle_refined_deg	2.532
r_nbtor_refined	0.322
r_symmetry_xyhbond_nbd_refined	0.241
r_nbd_refined	0.222
r_symmetry_nbd_refined	0.204
r_xyhbond_nbd_refined	0.167
r_chiral_restr	0.155
r_bond_refined_d	0.015
r_gen_planes_refined	0.015

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4659
Nucleic Acid Atoms
Solvent Atoms	321
Heterogen Atoms	112

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
Aimless	data scaling
PHASER	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 R01GM157729.