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L-ficolin complexed to N-acetyl-D-glucosamine
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 3.38 63.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 200.52 α = 90 b = 84.51 β = 123.57 c = 144.09 γ = 90
Symmetry Space Group C 1 2 1
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 2003-11-14 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 2.65 19.76 98.5 0.09 9.6 3.5 57851
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 2.65 19 51953 5886 100 0.234 0.228 0.2295 0.283 0.2806 RANDOM 55.89
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] 1.43 2.17 -0.13 1.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.116 r_dihedral_angle_4_deg 20.586 r_dihedral_angle_3_deg 19.147 r_dihedral_angle_1_deg 6.203 r_scangle_it 1.762 r_angle_refined_deg 1.402 r_scbond_it 1.325 r_mcangle_it 1.263 r_mcbond_it 0.82 r_symmetry_hbond_refined 0.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.116 r_dihedral_angle_4_deg 20.586 r_dihedral_angle_3_deg 19.147 r_dihedral_angle_1_deg 6.203 r_scangle_it 1.762 r_angle_refined_deg 1.402 r_scbond_it 1.325 r_mcangle_it 1.263 r_mcbond_it 0.82 r_symmetry_hbond_refined 0.4 r_nbtor_refined 0.336 r_symmetry_vdw_refined 0.269 r_nbd_refined 0.258 r_xyhbond_nbd_refined 0.214 r_chiral_restr 0.101 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 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 10412 Nucleic Acid Atoms Solvent Atoms 146 Heterogen Atoms 132
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling AMoRE phasing