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L-ficolin complexed to acetyl-choline
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 2.57 51.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.06 α = 90 b = 97.06 β = 90 c = 140 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 2004-09-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM16 ESRF BM16
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 2.85 19.96 94.9 0.08 11.7 3.1 32678
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 2.85 15 31443 1655 100 0.213 0.21 0.2063 0.275 0.2702 RANDOM 35.79
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] 1.12 0.56 1.12 -1.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.861 r_dihedral_angle_3_deg 19.221 r_dihedral_angle_4_deg 17.972 r_dihedral_angle_1_deg 6.634 r_scangle_it 1.664 r_mcangle_it 1.524 r_angle_refined_deg 1.399 r_scbond_it 1.109 r_mcbond_it 0.902 r_nbtor_refined 0.336
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.861 r_dihedral_angle_3_deg 19.221 r_dihedral_angle_4_deg 17.972 r_dihedral_angle_1_deg 6.634 r_scangle_it 1.664 r_mcangle_it 1.524 r_angle_refined_deg 1.399 r_scbond_it 1.109 r_mcbond_it 0.902 r_nbtor_refined 0.336 r_symmetry_hbond_refined 0.298 r_symmetry_vdw_refined 0.272 r_nbd_refined 0.254 r_xyhbond_nbd_refined 0.211 r_chiral_restr 0.099 r_bond_refined_d 0.012 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_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 10343 Nucleic Acid Atoms Solvent Atoms 90 Heterogen Atoms 123
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling AMoRE phasing