☰ Navigation Tabs
Crystal structure of the dimeric bH1-Fab variant [HC-Y33W,HC-D98F,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 tri-sodium citrate, pH 5.6, 12% PEG4000, 10% isopropanol
Crystal Properties Matthews coefficient Solvent content 3.41 63.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.679 α = 90 b = 95.96 β = 103.68 c = 110.11 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 1.95 50 99.1 0.223 0.261 0.134 0.947 26.6 3.7 95751
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 1.95 1.98 98.4 0.893 1.042 0.533 0.537 3.8
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 1.95 50 90638 4831 98.71 0.1932 0.1913 0.1995 0.2288 0.2335 RANDOM 29.286
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 -0.78 -0.94 -1.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.057 r_dihedral_angle_4_deg 18.81 r_dihedral_angle_3_deg 15.064 r_dihedral_angle_1_deg 7.536 r_angle_refined_deg 1.88 r_angle_other_deg 0.882 r_chiral_restr 0.115 r_bond_refined_d 0.02 r_gen_planes_refined 0.01 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.057 r_dihedral_angle_4_deg 18.81 r_dihedral_angle_3_deg 15.064 r_dihedral_angle_1_deg 7.536 r_angle_refined_deg 1.88 r_angle_other_deg 0.882 r_chiral_restr 0.115 r_bond_refined_d 0.02 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6649 Nucleic Acid Atoms Solvent Atoms 844 Heterogen Atoms 11
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction iMOSFLM data reduction MOLREP phasing