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Crystal Structure of Human Monocyte Chemoattractant Protein 4 (MCP-4/CCL13)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DOK PDB entry 1dok
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 0.1 M Bis-Tris, 2 M ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.06 40.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.673 α = 90 b = 74.673 β = 90 c = 51.65 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 300 mm CCD 2004-11-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.00 APS 22-ID
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 1.7 50 99.9 0.072 26.2 12.7 15683 15683 -3 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.76 99.5 0.568 2.6 5.4
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-Factor (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 PDB entry 1dok 1.7 30 14898 783 99.93 0.18155 0.17974 0.1819 0.21581 0.2159 RANDOM 31.722
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] -0.1 -0.1 0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.38 r_dihedral_angle_4_deg 21.215 r_dihedral_angle_3_deg 14.938 r_dihedral_angle_1_deg 5.558 r_scangle_it 4.687 r_scbond_it 3.383 r_mcangle_it 2.198 r_angle_refined_deg 1.926 r_mcbond_it 1.494 r_nbtor_refined 0.313
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.38 r_dihedral_angle_4_deg 21.215 r_dihedral_angle_3_deg 14.938 r_dihedral_angle_1_deg 5.558 r_scangle_it 4.687 r_scbond_it 3.383 r_mcangle_it 2.198 r_angle_refined_deg 1.926 r_mcbond_it 1.494 r_nbtor_refined 0.313 r_xyhbond_nbd_refined 0.241 r_nbd_refined 0.227 r_symmetry_vdw_refined 0.2 r_symmetry_hbond_refined 0.174 r_chiral_restr 0.149 r_bond_refined_d 0.02 r_gen_planes_refined 0.009 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_refined 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1038 Nucleic Acid Atoms Solvent Atoms 72 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling EPMR phasing