2XTJ | pdb_00002xtj

The crystal structure of PCSK9 in complex with 1D05 Fab

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2W2M	PDB ENTRY 2W2M

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION			CRYSTALLIZATION EXPERIMENTS WERE PERFORMED AT ROOM TEMPERATURE BY THE HANGING-DROP AND SITTING-DROP METHODS. THIN PLATE-LIKE CRYSTALS WERE OBTAINED IN 100 MM NA CITRATE PH 6.5, 13% PEG 6000. FOR DATA COLLECTION CRYSTALS WERE TRANSFERRED TO A STABILIZING SOLUTION (20 MM TRIS PH 8.0, 50 MM NACITRATE PH 6.5, 100 MM NACL, 5% GLYCEROL, 1 MM TCEP, 1 MICROM CACL2, 25% PEG6000), THEN TRANSFERRED FOR 2 MIN TO A CRYOPROTECTANT SOLUTION (20 MM TRIS PH 8.0, 50 MM NACITRATE PH 6.5, 100 MM NACL, 20% GLYCEROL, 1 MM TCEP, 1 MICROM CACL2, 35% PEG6000) AND FINALLY PLACED DIRECTLY INTO LIQUID NITROGEN.

Crystal Properties
Matthews coefficient	Solvent content
2.95	58.34

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.589	α = 90
b = 67.834	β = 90
c = 250.86	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	CCD	ADSC QUANTUM 4			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-2		ESRF	ID14-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.7	40	100	0.13	10.5	5.1		32238		2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.7	2.85	99.9		0.51	2.6	4.7

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 (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 2W2M	2.7	40	30522	1629	99.98	0.20293	0.19992	0.2	0.25944	0.26	RANDOM	34.08

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			-1.15		0.46

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.93
r_dihedral_angle_4_deg	20.378
r_dihedral_angle_3_deg	18.365
r_dihedral_angle_1_deg	7.414
r_scangle_it	2.353
r_angle_refined_deg	1.413
r_scbond_it	1.323
r_mcangle_it	1.051
r_mcbond_it	0.581
r_nbtor_refined	0.306
r_nbd_refined	0.222
r_symmetry_vdw_refined	0.207
r_xyhbond_nbd_refined	0.134
r_metal_ion_refined	0.133
r_chiral_restr	0.104
r_symmetry_hbond_refined	0.07
r_bond_refined_d	0.01
r_gen_planes_refined	0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5875
Nucleic Acid Atoms
Solvent Atoms	199
Heterogen Atoms	1

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing