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Crystal structure of AGAP1-GDP complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7EB6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIQUID DIFFUSION 298 10% w/v PEG 4000, 20% w/v 2-Propanol, 100 mM HEPES Sodium Salt, pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.94 58.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.405 α = 90 b = 124.678 β = 90 c = 127.604 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 CCD MAR CCD 300 mm 2021-03-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.987 SSRF BL17U
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 2.49 35.17 96.2 0.086 0.999 7.3 5.8 62085
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 2.49 2.579 1.57 0.685
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 2.49 35.17 2.01 62085 3144 95.8 0.221 0.219 0.2278 0.268 0.2662
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 15.43 f_angle_d 2.28 f_chiral_restr 0.176 f_bond_d 0.018 f_plane_restr 0.013
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10407 Nucleic Acid Atoms Solvent Atoms 64 Heterogen Atoms 245
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing PDB_EXTRACT data extraction