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Crystallographic structure of human C1q globular heads (P1)
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 2.13 41.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.15 α = 92.45 b = 48.24 β = 92.65 c = 87.79 γ = 113.53
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 ID29 ESRF ID29
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 1.95 44 95.8 0.04 16 2.15 50005
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 1.9 15 47553 5284 100 0.219 0.214 0.2183 0.26 0.2642 RANDOM 13.04
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] -0.36 0.13 0.13 -0.15 0.15 0.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.683 r_dihedral_angle_4_deg 16.912 r_dihedral_angle_3_deg 14.488 r_dihedral_angle_1_deg 6.622 r_scangle_it 2.483 r_scbond_it 1.898 r_mcangle_it 1.837 r_angle_refined_deg 1.582 r_mcbond_it 1.173 r_nbtor_refined 0.328
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.683 r_dihedral_angle_4_deg 16.912 r_dihedral_angle_3_deg 14.488 r_dihedral_angle_1_deg 6.622 r_scangle_it 2.483 r_scbond_it 1.898 r_mcangle_it 1.837 r_angle_refined_deg 1.582 r_mcbond_it 1.173 r_nbtor_refined 0.328 r_symmetry_vdw_refined 0.301 r_symmetry_hbond_refined 0.249 r_nbd_refined 0.241 r_xyhbond_nbd_refined 0.187 r_chiral_restr 0.118 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 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 6152 Nucleic Acid Atoms Solvent Atoms 109 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling