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Crystal Structure of the P-Rex2 PH domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5D27
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 295 0.1 M Sodium Acetate pH 5, 3.325 M Sodium Chloride
Crystal Properties Matthews coefficient Solvent content 2.36 47.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.105 α = 90 b = 60.105 β = 90 c = 86.238 γ = 120
Symmetry Space Group P 31 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 110 CCD MARMOSAIC 300 mm CCD 2015-04-23 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 1.9 52.05 99 0.064 0.069 0.024 10.1 7.2 14598
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 1.9 1.93 96.8 0.713 0.799 0.35 0.726 4.5
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 5D27 1.9 52.05 13861 736 99.12 0.1928 0.1908 0.201 0.2316 0.2466 RANDOM 36.253
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] -0.43 -0.22 -0.43 1.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.697 r_dihedral_angle_3_deg 13.631 r_dihedral_angle_4_deg 11.798 r_dihedral_angle_1_deg 6.532 r_angle_refined_deg 1.447 r_angle_other_deg 0.911 r_chiral_restr 0.096 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.697 r_dihedral_angle_3_deg 13.631 r_dihedral_angle_4_deg 11.798 r_dihedral_angle_1_deg 6.532 r_angle_refined_deg 1.447 r_angle_other_deg 0.911 r_chiral_restr 0.096 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1135 Nucleic Acid Atoms Solvent Atoms 74 Heterogen Atoms 4
Software Software Software Name Purpose HKL-2000 data collection HKL-2000 data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction PHASER phasing Coot model building