37HF | pdb_000037hf

X-RAY DIFFRACTION

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2QTW	Published PCSK9 structure, PDB 2QTW, used as molecular-replacement search model

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.8	293.15	0.10 M MD - Buffer System 1, pH 5.80, 13.00 % MD - Precipitant Mix 2, 2.50 % (v/v) MD - Cryopolyols , 90.00 mM MD - LiNaK Mix

Crystal Properties
Matthews coefficient	Solvent content
2.49	50.61

Symmetry
Space Group	P 21 2 21

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 X 16M		2025-10-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.91508	ESRF	ID23-1

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	2.07	109.45	40.6	0.54	0.59	0.24	0.98	4.2	11.5		35755

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.07	2.45	5.2		1.67	1.83	0.74	0.77	1.6	11.2

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 (All)	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	2QTW	2.072	109.447	35755	1829	40.62	0.331	0.331	0.3273	0.3091	0.405	0.3805	RANDOM	35.888

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]
6.334			-10.818		4.484

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	12.273
r_dihedral_angle_6_deg	9.15
r_dihedral_angle_2_deg	6.149
r_dihedral_angle_1_deg	5.066
r_lrange_it	4.017
r_lrange_other	3.939
r_mcangle_it	1.773
r_mcangle_other	1.773
r_scangle_it	1.385
r_scangle_other	1.385

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	12.273
r_dihedral_angle_6_deg	9.15
r_dihedral_angle_2_deg	6.149
r_dihedral_angle_1_deg	5.066
r_lrange_it	4.017
r_lrange_other	3.939
r_mcangle_it	1.773
r_mcangle_other	1.773
r_scangle_it	1.385
r_scangle_other	1.385
r_mcbond_it	1.001
r_mcbond_other	1.001
r_angle_refined_deg	0.802
r_scbond_it	0.766
r_scbond_other	0.766
r_angle_other_deg	0.317
r_symmetry_nbd_refined	0.235
r_symmetry_xyhbond_nbd_refined	0.225
r_nbd_other	0.19
r_symmetry_nbd_other	0.182
r_nbd_refined	0.16
r_nbtor_refined	0.16
r_xyhbond_nbd_refined	0.139
r_symmetry_nbtor_other	0.08
r_ncsr_local_group_1	0.065
r_chiral_restr	0.037
r_bond_refined_d	0.002
r_gen_planes_refined	0.002
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8277
Nucleic Acid Atoms
Solvent Atoms	504
Heterogen Atoms	32

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.