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Crystal structure of S25-39 Fab in complex with 4-MeO-KdoOAll
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3OKD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 289 0.1 M HEPES pH 7.0, 30% Jeffamine ED-2001, 5 mM 4-O-methyl-KdoOAll
Crystal Properties Matthews coefficient Solvent content 2.11 41.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.111 α = 90 b = 63.624 β = 97.4 c = 61.636 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV++ 2014-02-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE RIGAKU MICROMAX-003 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2 50 99.1 0.071 0.083 0.042 10.9 3.5 27284
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.07 95.1 0.398 0.472 0.248 0.853 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 3OKD 2 50 24109 1270 91.33 0.2169 0.2144 0.2614 0.2523 RANDOM 27.783
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] -0.35 -0.38 -0.21 0.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.142 r_dihedral_angle_4_deg 17.458 r_dihedral_angle_3_deg 15.153 r_dihedral_angle_1_deg 7.259 r_angle_refined_deg 1.495 r_angle_other_deg 0.824 r_chiral_restr 0.085 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.142 r_dihedral_angle_4_deg 17.458 r_dihedral_angle_3_deg 15.153 r_dihedral_angle_1_deg 7.259 r_angle_refined_deg 1.495 r_angle_other_deg 0.824 r_chiral_restr 0.085 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3330 Nucleic Acid Atoms Solvent Atoms 151 Heterogen Atoms 17
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling PDB_EXTRACT data extraction HKL-2000 data reduction PHASER phasing