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Crystal structure of the dimeric bH1-Fab variant [HC-Y33W,HC-D98M,HC-G99M]
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BDY PDB entry 3BDY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 5.6 295 0.1 M tris-sodium citrate, pH 5.6, 11% PEG4000, 8% isopropanol
Crystal Properties Matthews coefficient Solvent content 3.38 63.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.09 α = 90 b = 95.47 β = 103.01 c = 109.73 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 RAYONIX MX-300 2017-01-07 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 2.04 50 99.8 0.087 0.104 0.055 0.995 8.3 3.4 83010
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 2.04 2.08 99.5 0.571 0.678 0.363 0.75 3.4
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 PDB entry 3BDY 2.04 50 78804 4183 99.71 0.1686 0.1669 0.1756 0.2002 0.2067 RANDOM 32.147
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] 2.54 -0.51 0.05 -2.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.594 r_dihedral_angle_4_deg 17.007 r_dihedral_angle_3_deg 15.579 r_dihedral_angle_1_deg 7.187 r_angle_refined_deg 1.889 r_angle_other_deg 0.876 r_chiral_restr 0.112 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.594 r_dihedral_angle_4_deg 17.007 r_dihedral_angle_3_deg 15.579 r_dihedral_angle_1_deg 7.187 r_angle_refined_deg 1.889 r_angle_other_deg 0.876 r_chiral_restr 0.112 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6667 Nucleic Acid Atoms Solvent Atoms 722 Heterogen Atoms 7
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction iMOSFLM data reduction MOLREP phasing