6UMX

Structural basis for specific inhibition of extracellular activation of pro/latent myostatin by SRK-015

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5GGU	PDB entries 5GGU, 5F3H, 3HH2, 3RJR, & 5NTU
experimental model	PDB	5F3H	PDB entries 5GGU, 5F3H, 3HH2, 3RJR, & 5NTU
experimental model	PDB	3HH2	PDB entries 5GGU, 5F3H, 3HH2, 3RJR, & 5NTU
experimental model	PDB	3RJR	PDB entries 5GGU, 5F3H, 3HH2, 3RJR, & 5NTU
experimental model	PDB	5NTU	PDB entries 5GGU, 5F3H, 3HH2, 3RJR, & 5NTU

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	296	0.1 M sodium citrate, pH 5.5, 20% PEG3350, 15% 2-propanol, 3% trimethylamine N-oxide

Crystal Properties
Matthews coefficient	Solvent content
2.7	54.46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.62	α = 90
b = 110.01	β = 90
c = 293.27	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	93	PIXEL	DECTRIS PILATUS 6M		2017-08-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 17-ID	1.00000	APS	17-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim I (All)	Rpim I (All)	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	2.79	146.63	100	0.079	0.035	14.1	5.1		49196			79.718

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.79	2.84	100		1.487	0.645	1.2	5.3

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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entries 5GGU, 5F3H, 3HH2, 3RJR, & 5NTU	2.79	40.43	46728	2372	99.81	0.2193	0.217	0.2643	RANDOM	98.061

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]
-2.55			3.06		-0.51

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.928
r_dihedral_angle_4_deg	18.807
r_dihedral_angle_3_deg	18.752
r_dihedral_angle_1_deg	9.111
r_angle_refined_deg	2.072
r_angle_other_deg	1.171
r_chiral_restr	0.128
r_bond_refined_d	0.019
r_gen_planes_refined	0.011
r_bond_other_d	0.003

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.928
r_dihedral_angle_4_deg	18.807
r_dihedral_angle_3_deg	18.752
r_dihedral_angle_1_deg	9.111
r_angle_refined_deg	2.072
r_angle_other_deg	1.171
r_chiral_restr	0.128
r_bond_refined_d	0.019
r_gen_planes_refined	0.011
r_bond_other_d	0.003
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10841
Nucleic Acid Atoms
Solvent Atoms	2
Heterogen Atoms	6

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
xia2	data reduction

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.