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H-ficolin complexed to D-fucose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2J3G PDB ENTRY 2J3G
Crystallization Crystal Properties Matthews coefficient Solvent content 2.14 42.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62 α = 90 b = 62 β = 90 c = 346.8 γ = 90
Symmetry Space Group P 41 21 2
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 2005-11-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 ESRF ID14-1
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 1.8 46.22 99 0.12 12.5 6.9 29088
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 2J3G 1.8 15 54315 2858 100 0.214 0.212 0.2152 0.258 0.2634 RANDOM 33.67
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] 0.36 0.36 -0.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.004 r_dihedral_angle_4_deg 17.342 r_dihedral_angle_3_deg 14.785 r_dihedral_angle_1_deg 6.073 r_scangle_it 2.066 r_mcangle_it 1.747 r_scbond_it 1.557 r_angle_refined_deg 1.228 r_mcbond_it 1.137 r_nbtor_refined 0.323
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.004 r_dihedral_angle_4_deg 17.342 r_dihedral_angle_3_deg 14.785 r_dihedral_angle_1_deg 6.073 r_scangle_it 2.066 r_mcangle_it 1.747 r_scbond_it 1.557 r_angle_refined_deg 1.228 r_mcbond_it 1.137 r_nbtor_refined 0.323 r_symmetry_hbond_refined 0.26 r_symmetry_vdw_refined 0.257 r_nbd_refined 0.239 r_xyhbond_nbd_refined 0.201 r_chiral_restr 0.096 r_bond_refined_d 0.01 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 5055 Nucleic Acid Atoms Solvent Atoms 199 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling AMoRE phasing