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Crystal structure of bH1 Fab variant (CDR H3 loop design 13_0346) 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 Sodium acetate, 0.1 M HEPES pH 7.5, 20 %(w/v) PEG 3000
Crystal Properties Matthews coefficient Solvent content 2.89 57.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.459 α = 90 b = 99.409 β = 90 c = 191.219 γ = 90
Symmetry Space Group P 21 21 21
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 2018-05-10 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 2.32 95.61 99.7 0.089 0.1 0.045 0.996 10 4.9 63680
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 2.32 2.38 99.9 0.742 0.834 0.37 0.685 5
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 2.32 95.61 60457 3148 99.54 0.195 0.1924 0.1967 0.2462 0.2474 RANDOM 47.766
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] 0.79 1.8 -2.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.955 r_dihedral_angle_4_deg 25.885 r_dihedral_angle_3_deg 18.42 r_dihedral_angle_1_deg 7.006 r_angle_refined_deg 1.83 r_angle_other_deg 1.279 r_chiral_restr 0.101 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 r_bond_other_d 0.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.955 r_dihedral_angle_4_deg 25.885 r_dihedral_angle_3_deg 18.42 r_dihedral_angle_1_deg 7.006 r_angle_refined_deg 1.83 r_angle_other_deg 1.279 r_chiral_restr 0.101 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 r_bond_other_d 0.005 r_gen_planes_other 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8165 Nucleic Acid Atoms Solvent Atoms 486 Heterogen Atoms 9
Software Software Software Name Purpose REFMAC refinement SCALA data scaling PDB_EXTRACT data extraction iMOSFLM data reduction MOLREP phasing