3GV3

CXCL12 (SDF) in trigonal space group


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.53000.2 M LiSO4, 0.1 M Tris HCl, 30% PEG 4000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Crystal Properties
Matthews coefficientSolvent content
2.7455.17

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.51α = 90
b = 55.51β = 90
c = 45.963γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29A1.0809NSLSX29A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.648.0611094

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 REPLACEMENTTHROUGHOUT1.648.061040852298.710.206270.204290.24716RANDOM23.614
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]
0.920.460.92-1.38
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.942
r_dihedral_angle_4_deg24.537
r_dihedral_angle_3_deg16.991
r_dihedral_angle_1_deg6.871
r_scangle_it6.188
r_scbond_it3.868
r_mcangle_it2.981
r_angle_refined_deg2.405
r_mcbond_it1.77
r_chiral_restr0.195
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.942
r_dihedral_angle_4_deg24.537
r_dihedral_angle_3_deg16.991
r_dihedral_angle_1_deg6.871
r_scangle_it6.188
r_scbond_it3.868
r_mcangle_it2.981
r_angle_refined_deg2.405
r_mcbond_it1.77
r_chiral_restr0.195
r_bond_refined_d0.031
r_gen_planes_refined0.014
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_bond_other_d
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_sphericity_bonded
r_mcbond_other
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_rigid_bond_restr
r_sphericity_free
r_xyhbond_nbd_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms498
Nucleic Acid Atoms
Solvent Atoms58
Heterogen Atoms

Software

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