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Crystal Structure of A Viral Chemokine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1CM9 PDB ENTRY 1CM9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 vapor diffusion, sitting drops 1:1 10mg/ml protein: mother liquor (1.2M NaCl,0.1M NaOAc pH5.5, 22oC), vapor diffusion, sitting drops
Crystal Properties Matthews coefficient Solvent content 2.4 48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.452 α = 83.54 b = 40.636 β = 89.68 c = 55.092 γ = 79.19
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-1 SSRL BL9-1
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 94.7 0.044 14.8 28953
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 89.8 0.65 1.4
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 (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 1CM9 1.7 40 28953 26039 2914 90.3 0.194 0.189 0.198 0.236 0.2393 RANDOM 28.97
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] 0.02 0.01 0.13 -0.22 -0.06 0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.085 r_dihedral_angle_4_deg 17.444 r_dihedral_angle_3_deg 15.349 r_dihedral_angle_1_deg 7.097 r_scangle_it 5.212 r_scbond_it 4.226 r_mcangle_it 2.501 r_mcbond_it 2.389 r_angle_refined_deg 1.957 r_angle_other_deg 0.987
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.085 r_dihedral_angle_4_deg 17.444 r_dihedral_angle_3_deg 15.349 r_dihedral_angle_1_deg 7.097 r_scangle_it 5.212 r_scbond_it 4.226 r_mcangle_it 2.501 r_mcbond_it 2.389 r_angle_refined_deg 1.957 r_angle_other_deg 0.987 r_mcbond_other 0.477 r_symmetry_vdw_other 0.274 r_nbd_refined 0.219 r_nbd_other 0.208 r_xyhbond_nbd_refined 0.197 r_symmetry_hbond_refined 0.166 r_chiral_restr 0.134 r_symmetry_vdw_refined 0.11 r_nbtor_other 0.095 r_bond_refined_d 0.024 r_gen_planes_refined 0.009 r_bond_other_d 0.005 r_gen_planes_other 0.001 r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other 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 Atoms Number Protein Atoms 2204 Nucleic Acid Atoms Solvent Atoms 229 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing