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The crystal structure of BD1 in complex with BDS4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4LYS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 289.15 0.15 M potassium bromide, 30% (v/v) PEG2000MME
Crystal Properties Matthews coefficient Solvent content 1.88 34.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.114 α = 90 b = 55.444 β = 90 c = 57.53 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 PIXEL DECTRIS PILATUS 300K 2024-11-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CAMD BEAMLINE GCPCC 0.978 CAMD GCPCC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.461 29.98 99.69 0.998 15 9.8 20044 21.92
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 1.461 1.513 0.998
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.46206515118 29.9721530856 1.33554249965 19992 2002 99.710723192 0.169022743704 0.166075405785 0.1735 0.194724778156 0.1989 21.9232303211
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 17.4427069699 f_angle_d 1.39215247446 f_chiral_restr 0.0732517522019 f_bond_d 0.00684490587914 f_plane_restr 0.00519542980035
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1048 Nucleic Acid Atoms Solvent Atoms 145 Heterogen Atoms 34
Software Software Software Name Purpose PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling Coot model building