5VLK

Short PCSK9 delta-P' complex with shrunken peptide bearing homo-Arginine

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4NMX

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	292	calcium acetate, PEG 6000

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.387	α = 90
b = 70.387	β = 90
c = 156.983	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	110	PIXEL	DECTRIS PILATUS 6M		2017-01-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL12-2	0.97946	SSRL	BL12-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	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	2.2	50.01	100	0.111	16.1	9.9		23637		-3	32.2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.28	97.2		0.863	2.5	9.3

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	4NMX	2.2	50.01	22615	981	99.92	0.19702	0.19537	0.23703	RANDOM	33.642

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]
-0.8	-0.4		-0.8		2.6

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.764
r_dihedral_angle_4_deg	15.05
r_dihedral_angle_3_deg	13.245
r_long_range_B_refined	7.907
r_long_range_B_other	7.897
r_scangle_other	6.498
r_dihedral_angle_1_deg	5.9
r_mcangle_it	4.551
r_mcangle_other	4.55
r_scbond_it	4.157
r_scbond_other	4.156
r_mcbond_it	3.164
r_mcbond_other	3.126
r_angle_refined_deg	1.26
r_angle_other_deg	0.959
r_chiral_restr	0.065
r_gen_planes_refined	0.021
r_gen_planes_other	0.017
r_bond_refined_d	0.008
r_bond_other_d	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2869
Nucleic Acid Atoms
Solvent Atoms	213
Heterogen Atoms	2

Software

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