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Crystal structure of the P-Rex1 DEP1 domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1O7F PDB entry 1O7F
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293.15 0.1 M HEPES, pH 6.5, 45% w/v poly(acrylic acid sodium salt)2100
Crystal Properties Matthews coefficient Solvent content 4.76 74.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.152 α = 90 b = 103.152 β = 90 c = 67.981 γ = 120
Symmetry Space Group P 63 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 80 PIXEL DECTRIS PILATUS3 6M 2018-11-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.0332 APS 23-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) Rpim I (All) 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 3.12 50 99.3 0.152 0.049 19 8.4 4105
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.12 3.17 95.4 0.602 0.316 0.713 1.3 3
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 PDB entry 1O7F 3.12 19.62 3862 213 98.6 0.1855 0.1829 0.1859 0.2332 0.2292 RANDOM 105.74
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] -0.18 -0.09 -0.18 0.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.839 r_dihedral_angle_3_deg 19.909 r_dihedral_angle_1_deg 9.487 r_dihedral_angle_4_deg 9.04 r_angle_refined_deg 1.796 r_angle_other_deg 1.236 r_chiral_restr 0.065 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.839 r_dihedral_angle_3_deg 19.909 r_dihedral_angle_1_deg 9.487 r_dihedral_angle_4_deg 9.04 r_angle_refined_deg 1.796 r_angle_other_deg 1.236 r_chiral_restr 0.065 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 750 Nucleic Acid Atoms Solvent Atoms 4 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing