2XTJ

The crystal structure of PCSK9 in complex with 1D05 Fab


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2W2MPDB ENTRY 2W2M

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSIONCRYSTALLIZATION 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 coefficientSolvent content
2.9558.34

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 66.589α = 90
b = 67.834β = 90
c = 250.86γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 4MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-2ESRFID14-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.7401000.1310.55.1322382
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.72.8599.90.512.64.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 REPLACEMENTTHROUGHOUTPDB ENTRY 2W2M2.74030522162999.980.202930.199920.25944RANDOM34.08
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]
0.7-1.150.46
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.93
r_dihedral_angle_4_deg20.378
r_dihedral_angle_3_deg18.365
r_dihedral_angle_1_deg7.414
r_scangle_it2.353
r_angle_refined_deg1.413
r_scbond_it1.323
r_mcangle_it1.051
r_mcbond_it0.581
r_nbtor_refined0.306
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.93
r_dihedral_angle_4_deg20.378
r_dihedral_angle_3_deg18.365
r_dihedral_angle_1_deg7.414
r_scangle_it2.353
r_angle_refined_deg1.413
r_scbond_it1.323
r_mcangle_it1.051
r_mcbond_it0.581
r_nbtor_refined0.306
r_nbd_refined0.222
r_symmetry_vdw_refined0.207
r_xyhbond_nbd_refined0.134
r_metal_ion_refined0.133
r_chiral_restr0.104
r_symmetry_hbond_refined0.07
r_bond_refined_d0.01
r_gen_planes_refined0.004
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 AtomsNumber
Protein Atoms5875
Nucleic Acid Atoms
Solvent Atoms199
Heterogen Atoms1

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing