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Crystal structure of bH1 Fab variant (CDR H3 loop design 14_0130) in complex with VEGF
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BDY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 295 0.2 M Potassium chloride, 0.05 M HEPES pH 7.5, 35% (v/v) Pentaerythritol propoxylate
Crystal Properties Matthews coefficient Solvent content 2.98 58.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 194.167 α = 90 b = 100.749 β = 91.69 c = 153.509 γ = 90
Symmetry Space Group C 1 2 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 RAYONIX MX-300 2018-06-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.9795 CLSI 08ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.45 48.57 98.8 0.087 0.104 0.058 0.995 8.9 3.2 107303
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 2.45 2.49 98.2 0.628 0.757 0.418 0.571 3.2
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 FREE R-VALUE 3BDY 2.45 48.57 101921 5376 98.6 0.1911 0.1889 0.1939 0.2319 0.2361 RANDOM 46.514
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] -0.52 0.27 0.63 -0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.487 r_dihedral_angle_4_deg 22.365 r_dihedral_angle_3_deg 17.855 r_dihedral_angle_1_deg 7.095 r_angle_refined_deg 1.386 r_angle_other_deg 0.499 r_chiral_restr 0.066 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.487 r_dihedral_angle_4_deg 22.365 r_dihedral_angle_3_deg 17.855 r_dihedral_angle_1_deg 7.095 r_angle_refined_deg 1.386 r_angle_other_deg 0.499 r_chiral_restr 0.066 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16326 Nucleic Acid Atoms Solvent Atoms 811 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement SCALA data scaling PDB_EXTRACT data extraction iMOSFLM data reduction MOLREP phasing