2QTW

The Crystal Structure of PCSK9 at 1.9 Angstroms Resolution Reveals structural homology to Resistin within the C-terminal domain


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
110.529820% PEG6000, 0.2M sodium chloride, pH 10.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K, pH 10.50
Crystal Properties
Matthews coefficientSolvent content
2.2845.97

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.427α = 90
b = 70.149β = 90
c = 148.59γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152006-06-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.3ALS5.0.3

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.95099.90.0720.07222.5452284
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.91.9799.90.6990.6991.763.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.95049516265499.80.1940.1920.239RANDOM23.52
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]
-1.34-0.331.67
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.12
r_dihedral_angle_4_deg17.969
r_dihedral_angle_3_deg14.412
r_dihedral_angle_1_deg6.843
r_scangle_it6.216
r_scbond_it4.032
r_mcangle_it2.604
r_mcbond_it1.598
r_angle_refined_deg1.49
r_angle_other_deg0.902
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.12
r_dihedral_angle_4_deg17.969
r_dihedral_angle_3_deg14.412
r_dihedral_angle_1_deg6.843
r_scangle_it6.216
r_scbond_it4.032
r_mcangle_it2.604
r_mcbond_it1.598
r_angle_refined_deg1.49
r_angle_other_deg0.902
r_mcbond_other0.356
r_symmetry_vdw_other0.247
r_symmetry_hbond_refined0.225
r_nbd_refined0.205
r_nbd_other0.2
r_xyhbond_nbd_refined0.194
r_nbtor_refined0.179
r_metal_ion_refined0.175
r_symmetry_vdw_refined0.099
r_nbtor_other0.091
r_chiral_restr0.087
r_bond_refined_d0.015
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4347
Nucleic Acid Atoms
Solvent Atoms320
Heterogen Atoms15

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing