3OE0

Crystal structure of the CXCR4 chemokine receptor in complex with a cyclic peptide antagonist CVX15


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1LIPIDIC CUBIC PHASE7293Lipidic cubic phase made of monoolein and cholesterol, 25% PEG400, 0.3M Potassium sodium tartrate, 0.1 M Tris pH 7.0, LIPIDIC CUBIC PHASE, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.6266.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 82.08α = 90
b = 144.86β = 104.54
c = 73.99γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDmirrors2010-06-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-D1.0330APS23-ID-D

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
12.95094.90.129.5617656
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)
12.9373.60.631.53.9

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 REPLACEMENTTHROUGHOUT2.919.931670789895.240.217320.214630.26699RANDOM57.05
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]
0.10.2-0.410.41
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.366
r_dihedral_angle_3_deg18.646
r_dihedral_angle_4_deg15.924
r_dihedral_angle_1_deg5.801
r_scangle_it1.419
r_angle_refined_deg1.101
r_angle_other_deg0.855
r_scbond_it0.802
r_mcangle_it0.733
r_mcbond_it0.385
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.366
r_dihedral_angle_3_deg18.646
r_dihedral_angle_4_deg15.924
r_dihedral_angle_1_deg5.801
r_scangle_it1.419
r_angle_refined_deg1.101
r_angle_other_deg0.855
r_scbond_it0.802
r_mcangle_it0.733
r_mcbond_it0.385
r_chiral_restr0.06
r_mcbond_other0.045
r_bond_refined_d0.009
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
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 Atoms3634
Nucleic Acid Atoms
Solvent Atoms6
Heterogen Atoms

Software

Software
Software NamePurpose
Blu-Icedata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
SCALAdata scaling