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Complex between C1q globular heads and deoxyribose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PK6 PDB ENTRY 1PK6
Crystallization Crystal Properties Matthews coefficient Solvent content 2.14 42.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.35 α = 92.39 b = 48.33 β = 92.6 c = 88.06 γ = 113.57
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 ADSC QUANTUM 4 2008-05-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 ESRF ID14-2
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 1.25 50 83 0.06 19.15 1.7 167366 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 1.25 1.4 72.1 0.29 5.4 1.05
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 1PK6 1.25 19.71 158977 8368 100 0.17629 0.17496 0.1737 0.20176 0.2001 RANDOM 13.543
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] -0.44 -0.17 0.21 -0.62 0.15 0.96
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.566 r_dihedral_angle_3_deg 11.193 r_dihedral_angle_4_deg 10.278 r_dihedral_angle_1_deg 6.339 r_sphericity_bonded 2.314 r_sphericity_free 1.958 r_scangle_it 1.918 r_scbond_it 1.433 r_angle_refined_deg 1.095 r_mcangle_it 1.068
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.566 r_dihedral_angle_3_deg 11.193 r_dihedral_angle_4_deg 10.278 r_dihedral_angle_1_deg 6.339 r_sphericity_bonded 2.314 r_sphericity_free 1.958 r_scangle_it 1.918 r_scbond_it 1.433 r_angle_refined_deg 1.095 r_mcangle_it 1.068 r_rigid_bond_restr 0.761 r_mcbond_it 0.644 r_nbtor_refined 0.307 r_symmetry_vdw_refined 0.219 r_nbd_refined 0.216 r_symmetry_hbond_refined 0.181 r_xyhbond_nbd_refined 0.164 r_metal_ion_refined 0.095 r_chiral_restr 0.07 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 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_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6120 Nucleic Acid Atoms Solvent Atoms 1054 Heterogen Atoms 41
Software Software Software Name Purpose REFMAC refinement