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L-ficolin complexed to N-acetyl-D-galactosamine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JC9 PDB ENTRY 1JC9
Crystallization Crystal Properties Matthews coefficient Solvent content 2.58 52.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.825 α = 90 b = 96.825 β = 90 c = 141.898 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 2004-11-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM30A ESRF BM30A
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 2.8 19.92 96.8 0.08 11.9 3 35520
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 1JC9 2.8 15 34351 1808 100 0.224 0.222 0.2328 0.277 0.2964 RANDOM 41.92
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] 1.17 0.59 1.17 -1.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.676 r_dihedral_angle_3_deg 16.453 r_dihedral_angle_4_deg 14.566 r_dihedral_angle_1_deg 5.283 r_mcangle_it 0.945 r_angle_refined_deg 0.922 r_scangle_it 0.89 r_scbond_it 0.558 r_mcbond_it 0.537 r_symmetry_hbond_refined 0.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.676 r_dihedral_angle_3_deg 16.453 r_dihedral_angle_4_deg 14.566 r_dihedral_angle_1_deg 5.283 r_mcangle_it 0.945 r_angle_refined_deg 0.922 r_scangle_it 0.89 r_scbond_it 0.558 r_mcbond_it 0.537 r_symmetry_hbond_refined 0.36 r_nbtor_refined 0.33 r_symmetry_vdw_refined 0.295 r_nbd_refined 0.238 r_xyhbond_nbd_refined 0.218 r_metal_ion_refined 0.098 r_chiral_restr 0.068 r_bond_refined_d 0.005 r_gen_planes_refined 0.002 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10372 Nucleic Acid Atoms Solvent Atoms 53 Heterogen Atoms 220
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling AMoRE phasing