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Crystal structure of S25-2 Fab Unliganded 4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Q9K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 289 0.2 M Ammonium iodide, 20% PEG 3350, 5 mM 4-O-methoxymethyl-KdoOMe
Crystal Properties Matthews coefficient Solvent content 2.41 49.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.558 α = 90 b = 135.497 β = 94.26 c = 73.977 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 CCD MARMOSAIC 300 mm CCD 2015-06-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON OTHER 0.9795
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 40 99.8 0.092 0.107 0.054 9.2 4.1 122420
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 2.03 100 0.69 0.793 0.388 0.83 4.2
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 1Q9K 2 40 116254 6135 99.59 0.2232 0.2216 0.2262 0.2545 0.258 RANDOM 44.563
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] 3.05 0.25 -3.43 0.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.124 r_dihedral_angle_4_deg 16.773 r_dihedral_angle_3_deg 15.94 r_dihedral_angle_1_deg 6.597 r_angle_refined_deg 1.441 r_angle_other_deg 1.18 r_chiral_restr 0.09 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.124 r_dihedral_angle_4_deg 16.773 r_dihedral_angle_3_deg 15.94 r_dihedral_angle_1_deg 6.597 r_angle_refined_deg 1.441 r_angle_other_deg 1.18 r_chiral_restr 0.09 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.006 r_gen_planes_other 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13480 Nucleic Acid Atoms Solvent Atoms 389 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling PDB_EXTRACT data extraction HKL-2000 data reduction PHASER phasing