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Crystallographic structure of human C1q globular heads complexed to phosphatidyl-serine
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 2.74 54.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.09 α = 91.34 b = 48.07 β = 93.34 c = 84.7 γ = 113.68
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 CCD 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 2.05 19.95 89.7 0.04 13.5 1.92 38993
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 2.05 19.94 37012 1948 100 0.184 0.181 0.1832 0.241 0.2431 RANDOM 16.43
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] -0.55 -0.06 0.21 -0.95 -0.1 1.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.445 r_dihedral_angle_3_deg 13.649 r_dihedral_angle_4_deg 13.364 r_dihedral_angle_1_deg 6.184 r_scangle_it 1.553 r_mcangle_it 1.286 r_scbond_it 1.176 r_angle_refined_deg 1.028 r_mcbond_it 0.812 r_nbtor_refined 0.324
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.445 r_dihedral_angle_3_deg 13.649 r_dihedral_angle_4_deg 13.364 r_dihedral_angle_1_deg 6.184 r_scangle_it 1.553 r_mcangle_it 1.286 r_scbond_it 1.176 r_angle_refined_deg 1.028 r_mcbond_it 0.812 r_nbtor_refined 0.324 r_symmetry_vdw_refined 0.269 r_nbd_refined 0.231 r_xyhbond_nbd_refined 0.23 r_symmetry_hbond_refined 0.226 r_chiral_restr 0.069 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6239 Nucleic Acid Atoms Solvent Atoms 302 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling