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Crystal Structure of an N-terminally Truncated Linker-DH/PH Domains of p115-RhoGEF
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ODO PDB ENTRY 3ODO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 15-18% PEG 3350, 0.2M sodium chloride, and 0.1M NaHEPES, pH 6.2-6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.65 66.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.501 α = 90 b = 111.501 β = 90 c = 97.79 γ = 120
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 ADSC QUANTUM 210r Mirrors 2010-02-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.97921 APS 19-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 3.2 50 99.9 0.06 24.5 4.1 22503
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 3.2 3.26 100 0.58 2.1 4.1
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 3ODO 3.2 48.9 21259 1143 99.9 0.22742 0.22496 0.2248 0.27372 0.2484 RANDOM 111.37
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] 0.48 0.24 0.48 -0.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.148 r_dihedral_angle_4_deg 18.393 r_dihedral_angle_3_deg 17.289 r_dihedral_angle_1_deg 6.415 r_scangle_it 2.614 r_angle_refined_deg 1.736 r_scbond_it 1.453 r_mcangle_it 0.749 r_mcbond_it 0.359 r_chiral_restr 0.127
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.148 r_dihedral_angle_4_deg 18.393 r_dihedral_angle_3_deg 17.289 r_dihedral_angle_1_deg 6.415 r_scangle_it 2.614 r_angle_refined_deg 1.736 r_scbond_it 1.453 r_mcangle_it 0.749 r_mcbond_it 0.359 r_chiral_restr 0.127 r_bond_refined_d 0.02 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5516 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose HKL-3000 data collection PHASER phasing REFMAC refinement HKL-3000 data reduction HKL-2000 data scaling