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L-ficolin complexed to N-acetyl-cystein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2J3G PDP ENTRY 2J3G
Crystallization Crystal Properties Matthews coefficient Solvent content 2.54 51.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.04 α = 90 b = 99.04 β = 90 c = 142 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 ADSC CCD 2005-02-06 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 1.95 19.6 98.5 0.07 15 6.4 111804
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 PDP ENTRY 2J3G 1.95 15 107549 5661 100 0.178 0.176 0.1781 0.21 0.2119 RANDOM 38.77
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] 0.86 0.43 0.86 -1.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.264 r_dihedral_angle_4_deg 18.773 r_dihedral_angle_3_deg 14.451 r_dihedral_angle_1_deg 5.855 r_scangle_it 2.065 r_scbond_it 1.418 r_mcangle_it 1.324 r_angle_refined_deg 1.091 r_mcbond_it 0.88 r_nbtor_refined 0.323
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.264 r_dihedral_angle_4_deg 18.773 r_dihedral_angle_3_deg 14.451 r_dihedral_angle_1_deg 5.855 r_scangle_it 2.065 r_scbond_it 1.418 r_mcangle_it 1.324 r_angle_refined_deg 1.091 r_mcbond_it 0.88 r_nbtor_refined 0.323 r_symmetry_hbond_refined 0.252 r_xyhbond_nbd_refined 0.22 r_nbd_refined 0.217 r_symmetry_vdw_refined 0.199 r_chiral_restr 0.091 r_bond_refined_d 0.008 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 10249 Nucleic Acid Atoms Solvent Atoms 834 Heterogen Atoms 167
Software Software Software Name Purpose REFMAC refinement AMoRE phasing