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Crystal structure of CXCL12 in complex with inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2J7Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 2 M AmSO4, 2% MPD, 0.1 M MES Sodium Salt pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.42 49.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.93 α = 90 b = 57.71 β = 90 c = 72.53 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 93 IMAGE PLATE RIGAKU RAXIS IV 2011-09-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.9 45.16 99.8 0.061 21.77 6.89 12099
Refinement 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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2J7Z 1.9 20 12099 637 99.8 0.1863 0.1886 0.2347 0.2338 RANDOM 24.111
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] -0.09 0.12 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.8 r_dihedral_angle_4_deg 20.747 r_dihedral_angle_3_deg 11.827 r_long_range_B_refined 9.621 r_long_range_B_other 9.619 r_scangle_other 7.463 r_dihedral_angle_1_deg 6.554 r_scbond_it 5.672 r_scbond_other 5.305 r_mcangle_other 4.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.8 r_dihedral_angle_4_deg 20.747 r_dihedral_angle_3_deg 11.827 r_long_range_B_refined 9.621 r_long_range_B_other 9.619 r_scangle_other 7.463 r_dihedral_angle_1_deg 6.554 r_scbond_it 5.672 r_scbond_other 5.305 r_mcangle_other 4.03 r_mcangle_it 4.019 r_mcbond_it 3.067 r_mcbond_other 3.029 r_angle_refined_deg 1.822 r_angle_other_deg 1.375 r_chiral_restr 0.108 r_bond_refined_d 0.015 r_gen_planes_refined 0.01 r_bond_other_d 0.005 r_gen_planes_other 0.005 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1107 Nucleic Acid Atoms Solvent Atoms 40 Heterogen Atoms 31
Software Software Software Name Purpose XDS data scaling REFMAC refinement