☰ Navigation Tabs
Crystal structure of HDGFRP2 PWWP domain in complex with 4-(4-bromo-1H-pyrazol-3-yl) pyridine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other apo
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 278 0.01 M magnesium sulfate heptahydrate, 0.05 M sodium cacodylate trihydrate (pH 6.5), 2 M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.22 44.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.14 α = 90 b = 42.371 β = 90 c = 159.201 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 PILATUS3 6M 2023-07-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.97853 SSRF BL18U1
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 1.93 42.37 95.1 0.115 0.997 14.2 12.6 21227
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.93 1.98 100 0.906 0.898 2.9
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 THROUGHOUT 1.93 37.4 1.34 21126 1003 94.99 0.1912 0.189 0.189 0.2358 0.2362
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 7.172 f_angle_d 0.939 f_chiral_restr 0.058 f_plane_restr 0.009 f_bond_d 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2183 Nucleic Acid Atoms Solvent Atoms 153 Heterogen Atoms 61
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling MOLREP phasing PDB_EXTRACT data extraction