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Crystal Structure of the P-Rex1 PH domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5D3V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.7 294 Bis Tris, Magnesium chloride, PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.23 44.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.897 α = 90 b = 39.897 β = 90 c = 187.269 γ = 120
Symmetry Space Group P 32 1 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 CCD MARMOSAIC 300 mm CCD 2014-02-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.078 APS 21-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.92 30 97.9 0.091 0.097 0.035 11.8 7.7 13243
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 1.92 1.95 96.9 0.668 0.716 0.255 0.861 7.7 631
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 5D3V 1.92 30 12588 655 98.33 0.1899 0.1877 0.1973 0.2317 0.2382 RANDOM 35.438
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] -0.17 -0.09 -0.17 0.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.272 r_dihedral_angle_4_deg 20.711 r_dihedral_angle_3_deg 15.26 r_dihedral_angle_1_deg 6.02 r_mcangle_it 3.351 r_mcbond_it 2.283 r_mcbond_other 2.279 r_angle_refined_deg 1.525 r_angle_other_deg 0.923 r_chiral_restr 0.092
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.272 r_dihedral_angle_4_deg 20.711 r_dihedral_angle_3_deg 15.26 r_dihedral_angle_1_deg 6.02 r_mcangle_it 3.351 r_mcbond_it 2.283 r_mcbond_other 2.279 r_angle_refined_deg 1.525 r_angle_other_deg 0.923 r_chiral_restr 0.092 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1251 Nucleic Acid Atoms Solvent Atoms 92 Heterogen Atoms 1
Software Software Software Name Purpose HKL-2000 data scaling HKL-2000 data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement Coot model building PDB_EXTRACT data extraction