4NMX | pdb_00004nmx

PCSK9(deltaCRD) in complex with phage-derived inhibitory peptide 2-8

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2QTW	PDB ENTRY 2QTW

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	292	0.1 M lithium chloride, 10% w/v PEG6000, 0.05 M Tris, pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 292K

Crystal Properties
Matthews coefficient	Solvent content
2.43	49.32

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 95.102	α = 90
b = 70.765	β = 96.08
c = 70.413	γ = 90

Symmetry
Space Group	C 1 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	103	CCD	MARMOSAIC 325 mm CCD		2011-05-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.979	SSRL	BL9-2

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	1.85	50	99.9	0.099	11	3.8	39638	39638		-3	15

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.85

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2QTW	1.85	37.42	38618	38618	1020	99.8	0.18633	0.18539	0.1921	0.22237	0.2308	RANDOM	18.627

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]
0.7		0.05	-0.82		0.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.536
r_dihedral_angle_4_deg	18.207
r_dihedral_angle_3_deg	12.801
r_dihedral_angle_1_deg	5.23
r_angle_refined_deg	1.102
r_angle_other_deg	0.864
r_chiral_restr	0.064
r_bond_refined_d	0.008
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2916
Nucleic Acid Atoms
Solvent Atoms	378
Heterogen Atoms

Software

Software
Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling