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Afamin antibody fragment, N14 Fab, L1- glycosilated, crystal form II, same as 5L7X, but isomorphous setting indexed same as 5L88, 5L9D
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, HANGING DROP 5.5 291 200 NL FAB (10MG/ML IN 20 MM HEPES PH
7.5, 150 MM NACL) PLUS 200 NL COCKTAIL (30% PEG 1K, 200MM
AMMONIUM FLUORIDE, NH4F, pH 5.5), VAPOR DIFFUSION, SITTING DROP,
TEMPERATURE 291K
Crystal Properties Matthews coefficient Solvent content 2.3 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.196 α = 90 b = 67.491 β = 90 c = 88.941 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 PILATUS3 6M TORROIDAL MIRROR SI(111) 2015-06-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 1.0000 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 1.86 44.47 98.6 0.074 8.8 3.9 36491 40
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 1.86 1.93 91.3 0.934 1 3
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1IL1 1.86 47.06 34797 1783 98.4 0.192 0.19 0.228 0.2181 RANDOM 39.38
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] -0.28 -0.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.021 r_dihedral_angle_4_deg 18.653 r_dihedral_angle_3_deg 14.261 r_long_range_B_refined 6.854 r_long_range_B_other 6.852 r_dihedral_angle_1_deg 6.772 r_scangle_other 3.577 r_scbond_it 2.421 r_scbond_other 2.392 r_mcangle_other 2.263
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.021 r_dihedral_angle_4_deg 18.653 r_dihedral_angle_3_deg 14.261 r_long_range_B_refined 6.854 r_long_range_B_other 6.852 r_dihedral_angle_1_deg 6.772 r_scangle_other 3.577 r_scbond_it 2.421 r_scbond_other 2.392 r_mcangle_other 2.263 r_mcangle_it 2.262 r_angle_refined_deg 1.501 r_mcbond_it 1.479 r_mcbond_other 1.476 r_angle_other_deg 0.9 r_chiral_restr 0.088 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 3224 Nucleic Acid Atoms Solvent Atoms 223 Heterogen Atoms 64
Software Software Software Name Purpose REFMAC refinement XDS data reduction autoPROC data reduction XSCALE data scaling Aimless data scaling BALBES phasing