☰ Navigation Tabs
Crystal structure of BAY-297 with PIP4K2A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2YBX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 16% PEG 3350, 200mM Magnesium formate, 25% glycerol
Crystal Properties Matthews coefficient Solvent content 2.51 50.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.984 α = 90 b = 99.26 β = 93.37 c = 104.191 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 PIXEL DECTRIS PILATUS 6M 2019-07-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.0332 PETRA III, DESY P11
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.95 104.09 98.6 0.091 9.26 2.86 64335
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 2.07 0.539
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 2YBX 1.95 46.07 62224 2100 98.56 0.2011 0.1995 0.2102 0.2475 0.2526 RANDOM 42.065
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] -1.24 1.24 1.17 -0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.813 r_dihedral_angle_4_deg 17.52 r_dihedral_angle_3_deg 15.815 r_dihedral_angle_1_deg 7.584 r_angle_refined_deg 1.826 r_angle_other_deg 1.362 r_chiral_restr 0.083 r_bond_refined_d 0.014 r_gen_planes_refined 0.01 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.813 r_dihedral_angle_4_deg 17.52 r_dihedral_angle_3_deg 15.815 r_dihedral_angle_1_deg 7.584 r_angle_refined_deg 1.826 r_angle_other_deg 1.362 r_chiral_restr 0.083 r_bond_refined_d 0.014 r_gen_planes_refined 0.01 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5234 Nucleic Acid Atoms Solvent Atoms 172 Heterogen Atoms 84
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling MOLREP phasing