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H-ficolin complexed to galactose
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 2.07 40
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.2 α = 90 b = 62.2 β = 90 c = 345.49 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 1.7 46.22 98.1 0.07 17.7 7.6 74677
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 1.73 19 68814 3622 100 0.204 0.202 0.204 0.233 0.2357 RANDOM 24.22
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] 0.54 0.54 -1.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 24.012 r_dihedral_angle_4_deg 17.325 r_dihedral_angle_3_deg 13.832 r_dihedral_angle_1_deg 5.611 r_scangle_it 2.083 r_mcangle_it 1.639 r_scbond_it 1.461 r_mcbond_it 1.099 r_angle_refined_deg 1.047 r_nbtor_refined 0.319
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 24.012 r_dihedral_angle_4_deg 17.325 r_dihedral_angle_3_deg 13.832 r_dihedral_angle_1_deg 5.611 r_scangle_it 2.083 r_mcangle_it 1.639 r_scbond_it 1.461 r_mcbond_it 1.099 r_angle_refined_deg 1.047 r_nbtor_refined 0.319 r_symmetry_hbond_refined 0.247 r_nbd_refined 0.224 r_symmetry_vdw_refined 0.211 r_xyhbond_nbd_refined 0.192 r_chiral_restr 0.084 r_bond_refined_d 0.007 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 5035 Nucleic Acid Atoms Solvent Atoms 485 Heterogen Atoms 19
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling AMoRE phasing