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Structure of an Anti-Methotrexate CDR1-4 Graft VHH Antibody in Complex with Methotrexate
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293.15 0.2M Lithium Sulfate Monohydrate, 0.1M Tris. 25% w/v PEG 3,350, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K
Crystal Properties Matthews coefficient Solvent content 2.4 48.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.669 α = 90 b = 57.605 β = 90.27 c = 131.136 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 MAR 225 2010-07-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM 0.979 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 2.5 20 99.5 0.076 8.73 3.4 37495 2
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 MIR THROUGHOUT 2.5 20 37250 35361 1859 98.75 0.23209 0.22955 0.2229 0.27855 0.2673 RANDOM 48.323
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] 5.31 1.09 -0.23 -5.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.844 r_dihedral_angle_3_deg 19.828 r_dihedral_angle_4_deg 18.836 r_dihedral_angle_1_deg 7.884 r_scangle_it 3.264 r_scbond_it 2.375 r_mcangle_it 1.536 r_angle_refined_deg 1.518 r_mcbond_it 0.943 r_chiral_restr 0.116
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.844 r_dihedral_angle_3_deg 19.828 r_dihedral_angle_4_deg 18.836 r_dihedral_angle_1_deg 7.884 r_scangle_it 3.264 r_scbond_it 2.375 r_mcangle_it 1.536 r_angle_refined_deg 1.518 r_mcbond_it 0.943 r_chiral_restr 0.116 r_bond_refined_d 0.015 r_gen_planes_refined 0.011 r_bond_other_d r_angle_other_deg 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 4688 Nucleic Acid Atoms Solvent Atoms 53 Heterogen Atoms 173
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling