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Human synthetic monocyte chemoattractant protein 1 (MCP-1)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DOL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 0.1 M TRIS PH 8.5, 2.4 M K/NA PHOSPHATE, 2% PEG 400 CRYO CONDITIONS: 0.1 M TRIS PH 8.5, 2.2 M K/NA PHOSPHATE, 2% PEG 400, 17% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.78 56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.71 α = 90 b = 60.71 β = 90 c = 45.49 γ = 120
Symmetry Space Group P 32 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 107 CCD RIGAKU SATURN 944 VARIMAX HF 2007-03-14 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 34.4 80.8 0.051 1.9 6396 -4 35.2
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) 1.9 1.97 39.7 0.52 1.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1DOL 1.9 15 6079 6079 294 76.2 0.19534 0.19534 0.19264 0.1956 0.25467 0.256 RANDOM 48.3
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] -0.05 -0.03 -0.05 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.558 r_scangle_it 14.306 r_dihedral_angle_3_deg 14.193 r_dihedral_angle_4_deg 11.984 r_scbond_it 9.681 r_dihedral_angle_1_deg 6.171 r_mcangle_it 3.919 r_mcbond_it 2.265 r_angle_refined_deg 1.248 r_nbtor_refined 0.294
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.558 r_scangle_it 14.306 r_dihedral_angle_3_deg 14.193 r_dihedral_angle_4_deg 11.984 r_scbond_it 9.681 r_dihedral_angle_1_deg 6.171 r_mcangle_it 3.919 r_mcbond_it 2.265 r_angle_refined_deg 1.248 r_nbtor_refined 0.294 r_symmetry_vdw_refined 0.269 r_nbd_refined 0.219 r_symmetry_hbond_refined 0.168 r_xyhbond_nbd_refined 0.158 r_metal_ion_refined 0.116 r_chiral_restr 0.087 r_symmetry_metal_ion_refined 0.059 r_bond_refined_d 0.011 r_gen_planes_refined
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 527 Nucleic Acid Atoms Solvent Atoms 14 Heterogen Atoms 6
Software Software Software Name Purpose d*TREK data scaling AMoRE phasing REFMAC refinement d*TREK data reduction