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ArhGAP9 PH domain in complex with Ins(1,3,5)P3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DRO pdb entry 1DRO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 20% PEG4000, 100mM HEPES, 5% glycerol, 5mM DTT, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.12 42.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 28.751 α = 90 b = 36.601 β = 90 c = 113.708 γ = 90
Symmetry Space Group P 21 21 21
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 315 bent-flat Si-mirror (Rh coated) 2004-03-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-C 0.90020 APS 14-BM-C
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 1.9 25 93.1 0.055 18.4 5.8 9223
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) 1.9 1.97 91.3 0.291
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 1DRO 1.91 20 8744 438 92.85 0.21028 0.2093 0.2086 0.23014 0.2236 RANDOM 20.745
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] -0.66 1.46 -0.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.551 r_dihedral_angle_4_deg 21.242 r_dihedral_angle_3_deg 13.833 r_dihedral_angle_1_deg 5.971 r_scangle_it 5.251 r_scbond_it 3.248 r_mcangle_it 2.023 r_mcbond_it 1.844 r_angle_refined_deg 1.68 r_nbtor_refined 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.551 r_dihedral_angle_4_deg 21.242 r_dihedral_angle_3_deg 13.833 r_dihedral_angle_1_deg 5.971 r_scangle_it 5.251 r_scbond_it 3.248 r_mcangle_it 2.023 r_mcbond_it 1.844 r_angle_refined_deg 1.68 r_nbtor_refined 0.3 r_symmetry_hbond_refined 0.284 r_symmetry_vdw_refined 0.245 r_nbd_refined 0.22 r_xyhbond_nbd_refined 0.176 r_chiral_restr 0.119 r_bond_refined_d 0.017 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other 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 927 Nucleic Acid Atoms Solvent Atoms 48 Heterogen Atoms 5
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction