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Structure of an Anti-Methotrexate CDR1-3 Graft VHH Antibody in Complex with Methotrexate
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 293.15 1.0M Succinic Acid, 0.1M HEPES, 1% w/v PEG 2,000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K
Crystal Properties Matthews coefficient Solvent content 4.39 72.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.063 α = 90 b = 103.063 β = 90 c = 157.073 γ = 120
Symmetry Space Group P 61 2 2
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 MAR 225 2010-02-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM APS 22-BM
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 1.7 20 96.5 0.067 34.4 10.8 52887 2.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) 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 1.7 20 50174 50174 2698 96.4 0.176 0.175 0.1848 0.195 0.2046 RANDOM 26.09
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] 1.03 0.52 1.03 -1.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.992 r_dihedral_angle_4_deg 18.669 r_dihedral_angle_3_deg 15.082 r_scangle_it 6.569 r_dihedral_angle_1_deg 5.517 r_scbond_it 4.484 r_mcangle_it 3.014 r_angle_refined_deg 2.499 r_angle_other_deg 2.043 r_mcbond_it 1.811
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.992 r_dihedral_angle_4_deg 18.669 r_dihedral_angle_3_deg 15.082 r_scangle_it 6.569 r_dihedral_angle_1_deg 5.517 r_scbond_it 4.484 r_mcangle_it 3.014 r_angle_refined_deg 2.499 r_angle_other_deg 2.043 r_mcbond_it 1.811 r_chiral_restr 0.329 r_bond_refined_d 0.033 r_gen_planes_refined 0.015 r_bond_other_d 0.008 r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1904 Nucleic Acid Atoms Solvent Atoms 222 Heterogen Atoms 71
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement DENZO data reduction SCALA data scaling