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Crystal structure of the human RalGAPA2 N-terminal domain with human kappaB-Ras1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold generated on a local installation
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 277 17 % PEG 3350
20 % glycerol
0.1 M MgCl2
1 ul protei + 1 ul screening buffer + 1 ul seed
seed (1:200)
Crystal Properties Matthews coefficient Solvent content 2.77 55.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 163.564 α = 90 b = 63.43 β = 91.263 c = 104.163 γ = 90
Symmetry Space Group C 1 2 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 EIGER2 X 16M 2023-08-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) 0.68879 PETRA III, EMBL c/o DESY P14 (MX2)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.716 104.138 91.5 0.114 0.125 0.052 0.997 10.2 5.56 21842 65.48
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.716 2.959 57.9 1.202 1.363 0.632 0.508 4.56
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 2.72 63.63 1.33 21829 1118 74.91 0.1976 0.1951 0.1928 0.253 0.2528 65.48
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 19.2746 f_angle_d 0.5289 f_chiral_restr 0.0372 f_plane_restr 0.0039 f_bond_d 0.0029
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6404 Nucleic Acid Atoms Solvent Atoms 32 Heterogen Atoms 66
Software Software Software Name Purpose PHENIX refinement autoPROC data processing Aimless data scaling STARANISO data scaling XDS data reduction PHASER phasing Coot model building