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Complement factor H in complex with the GM1 glycan
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3OXU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 0.1 M TRIS-HCL, PH 9.0, 8% W/V PRG 8000
Crystal Properties Matthews coefficient Solvent content 2.88 57.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.77 α = 112.97 b = 82.86 β = 111.43 c = 86.57 γ = 99.63
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 2M-F 2013-11-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.0 SLS X06DA
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 2.24 50 97.6 0.0525 15.6 3.5 79286
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 2.24 2.3 97.1 0.611 1.99 3.4
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 3OXU 2.24 46.18 75320 3965 98.02 0.18326 0.1809 0.19 0.22835 0.2345 RANDOM 68.98
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] -2.18 1.33 1.11 -3.57 0.3 1.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.508 r_dihedral_angle_4_deg 16.705 r_dihedral_angle_3_deg 15.486 r_long_range_B_refined 11.158 r_long_range_B_other 11.158 r_scangle_other 8.917 r_mcangle_it 7.848 r_mcangle_other 7.847 r_dihedral_angle_1_deg 6.28 r_scbond_it 6.181
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.508 r_dihedral_angle_4_deg 16.705 r_dihedral_angle_3_deg 15.486 r_long_range_B_refined 11.158 r_long_range_B_other 11.158 r_scangle_other 8.917 r_mcangle_it 7.848 r_mcangle_other 7.847 r_dihedral_angle_1_deg 6.28 r_scbond_it 6.181 r_scbond_other 6.179 r_mcbond_it 5.621 r_mcbond_other 5.611 r_angle_refined_deg 1.387 r_angle_other_deg 1.051 r_chiral_restr 0.08 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_gen_planes_other 0.006 r_bond_other_d 0.005 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9610 Nucleic Acid Atoms Solvent Atoms 448 Heterogen Atoms 181
Software Software Software Name Purpose REFMAC refinement XDS data reduction Coot model building XSCALE data scaling PHASER phasing