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Crystal Structure of the DH/PH domains of p115-RhoGEF (R399E mutant)
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 1 293 2.7-3.0M sodium formate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.98 69.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.823 α = 90 b = 110.823 β = 90 c = 98.565 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 IMAGE PLATE RIGAKU RAXIS IV++ 2010-10-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT
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 2.5 50 99.9 0.091 22.7 3.6 46979
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) 2.5 2.54 99.4 0.58 2.1 2.7
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 2.5 48.3 44566 2372 99.9 0.228 0.226 0.2225 0.266 0.2618 RANDOM 48.66
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] 0.09 0.04 0.09 -0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.159 r_dihedral_angle_4_deg 23.863 r_dihedral_angle_3_deg 19.352 r_dihedral_angle_1_deg 6.547 r_scangle_it 4.86 r_scbond_it 3.073 r_angle_refined_deg 2.012 r_mcangle_it 1.571 r_mcbond_it 0.831 r_chiral_restr 0.148
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.159 r_dihedral_angle_4_deg 23.863 r_dihedral_angle_3_deg 19.352 r_dihedral_angle_1_deg 6.547 r_scangle_it 4.86 r_scbond_it 3.073 r_angle_refined_deg 2.012 r_mcangle_it 1.571 r_mcbond_it 0.831 r_chiral_restr 0.148 r_bond_refined_d 0.023 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 5653 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling