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Crystal structure of the Ras-associating and pleckstrin-homology domains of RIAM
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3HK0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 298 12% PEG3350, 100 mM LiAc, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.34 47.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.86 α = 90 b = 82.389 β = 95.19 c = 83.404 γ = 90
Symmetry Space Group P 1 21 1
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 4r 2010-04-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X4A NSLS X4A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.35 50 91.7 0.059 0.059 19 2.9 22885 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.35 2.39 98.3 0.275 0.291 3.2 2.9
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 3HK0 2.35 50 22885 1222 91.4 0.236 0.234 0.2304 0.282 0.2753 RANDOM 27.18
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] 0.26 0.3 -2.33 2.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.802 r_dihedral_angle_4_deg 13.76 r_dihedral_angle_3_deg 13.065 r_dihedral_angle_1_deg 4.575 r_angle_refined_deg 0.866 r_scangle_it 0.721 r_scbond_it 0.415 r_mcangle_it 0.398 r_mcbond_it 0.213 r_chiral_restr 0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.802 r_dihedral_angle_4_deg 13.76 r_dihedral_angle_3_deg 13.065 r_dihedral_angle_1_deg 4.575 r_angle_refined_deg 0.866 r_scangle_it 0.721 r_scbond_it 0.415 r_mcangle_it 0.398 r_mcbond_it 0.213 r_chiral_restr 0.06 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 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 3995 Nucleic Acid Atoms Solvent Atoms 239 Heterogen Atoms
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling