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AFAMIN ANTIBODY FRAGMENT, N14 FAB, L1- GLYCOSILATED, CRYSTAL FORM I, non-parsimonious model
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1IL1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 5.8 291 200nL Fab 10mg/ml in 20 mM HEPES pH 7.5, 150 mM NaCl plus
200nL 30%w/v PEG 1k, 200mM KF, pH 5.8)
Crystal Properties Matthews coefficient Solvent content 2.19 43.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.782 α = 90 b = 69.249 β = 90 c = 87.803 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M Torroidal focussing mirror 2015-06-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 1.000 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 1.88 54.37 99.4 0.076 0.998 10 4.5 34249 36.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.88 1.95 97.7 0.8 1.4 3.2
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 1IL1 1.88 47.38 32346 1659 99.14 0.17212 0.17003 0.1795 0.21145 0.215 RANDOM 37.307
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] 1.77 -0.54 -1.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.173 r_dihedral_angle_4_deg 22.755 r_dihedral_angle_3_deg 13.579 r_long_range_B_refined 6.723 r_long_range_B_other 6.722 r_dihedral_angle_1_deg 6.436 r_scangle_other 4.647 r_scbond_it 3.171 r_scbond_other 3.169 r_mcangle_other 3.143
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.173 r_dihedral_angle_4_deg 22.755 r_dihedral_angle_3_deg 13.579 r_long_range_B_refined 6.723 r_long_range_B_other 6.722 r_dihedral_angle_1_deg 6.436 r_scangle_other 4.647 r_scbond_it 3.171 r_scbond_other 3.169 r_mcangle_other 3.143 r_mcangle_it 3.136 r_mcbond_it 2.102 r_mcbond_other 2.089 r_angle_refined_deg 1.377 r_angle_other_deg 0.865 r_chiral_restr 0.081 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3300 Nucleic Acid Atoms Solvent Atoms 252 Heterogen Atoms 189
Software Software Software Name Purpose REFMAC refinement autoPROC data collection autoPROC data scaling XDS data reduction SCALA data scaling BALBES phasing Coot model building WARP model building