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Short wilavidin biotin complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7OUQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 1.5-1.7 M ammonium sulfate
0.1 M HEPES at pH 7.5
2-3% PEG 400
Crystal Properties Matthews coefficient Solvent content 2.29 46.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.555 α = 90 b = 67.384 β = 90 c = 77.789 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 2M 2021-05-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.96546 ESRF MASSIF-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.666 77.79 99.6 0.106 0.998 10.1 6.5 55507
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.666 1.695 0.901
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 7OUQ 1.67 77.79 52626 2766 99.38 0.1923 0.1893 0.2026 0.251 0.2603 RANDOM 16.459
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] 0.76 -1.07 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.248 r_dihedral_angle_3_deg 11.005 r_dihedral_angle_4_deg 10.886 r_dihedral_angle_1_deg 7.758 r_rigid_bond_restr 3.736 r_angle_refined_deg 2.169 r_angle_other_deg 1.566 r_chiral_restr 0.097 r_bond_refined_d 0.018 r_gen_planes_refined 0.012
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.248 r_dihedral_angle_3_deg 11.005 r_dihedral_angle_4_deg 10.886 r_dihedral_angle_1_deg 7.758 r_rigid_bond_restr 3.736 r_angle_refined_deg 2.169 r_angle_other_deg 1.566 r_chiral_restr 0.097 r_bond_refined_d 0.018 r_gen_planes_refined 0.012 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3292 Nucleic Acid Atoms Solvent Atoms 153 Heterogen Atoms 155
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction autoPROC data reduction PHASER phasing