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L-ficolin complexed to N-acetylglucosamine (forme C)
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 3.16 60.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.591 α = 90 b = 79.591 β = 90 c = 172.04 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 CCD MARRESEARCH 2004-04-04 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 2.7 19.39 99.8 0.05 24.6 6.9 16911
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 2.7 15 15836 990 100 0.212 0.207 0.2047 0.291 0.285 RANDOM 56.49
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] 3.03 1.52 3.03 -4.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 8.238 r_scangle_it 3.4 r_mcangle_it 2.444 r_scbond_it 2.252 r_angle_refined_deg 2.043 r_mcbond_it 1.349 r_nbd_refined 0.295 r_xyhbond_nbd_refined 0.274 r_symmetry_hbond_refined 0.271 r_symmetry_vdw_refined 0.258
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 8.238 r_scangle_it 3.4 r_mcangle_it 2.444 r_scbond_it 2.252 r_angle_refined_deg 2.043 r_mcbond_it 1.349 r_nbd_refined 0.295 r_xyhbond_nbd_refined 0.274 r_symmetry_hbond_refined 0.271 r_symmetry_vdw_refined 0.258 r_chiral_restr 0.135 r_bond_refined_d 0.019 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_refined 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 3458 Nucleic Acid Atoms Solvent Atoms 62 Heterogen Atoms 17
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling AMoRE phasing