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ArhGAP9 PH domain in complex with Ins(1,3,4)P3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2P0F pdb entry 2P0F
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 20% PEG4000, 100 mM HEPES, 5% glycerol, 5mM DTT, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.11 41.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 28.92 α = 90 b = 36.55 β = 90 c = 112.02 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 IMAGE PLATE MAR scanner 345 mm plate bent-flat Si-mirror (Rh coated) 2004-11-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-ID-B 1.12714 APS 14-ID-B
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 55.989 99.9 0.044 12.6 13.3 9930 9921
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 2 99.3 0.225 3.33
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 2P0F 1.9 28.01 9443 476 99.94 0.19677 0.19435 0.1935 0.2458 0.2458 RANDOM 19.86
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] 0.1 -0.01 -0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.388 r_dihedral_angle_4_deg 21.364 r_dihedral_angle_3_deg 15.707 r_dihedral_angle_1_deg 6.664 r_scangle_it 5.07 r_scbond_it 3.347 r_angle_refined_deg 2.161 r_mcangle_it 2.114 r_mcbond_it 1.351 r_nbtor_refined 0.316
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.388 r_dihedral_angle_4_deg 21.364 r_dihedral_angle_3_deg 15.707 r_dihedral_angle_1_deg 6.664 r_scangle_it 5.07 r_scbond_it 3.347 r_angle_refined_deg 2.161 r_mcangle_it 2.114 r_mcbond_it 1.351 r_nbtor_refined 0.316 r_nbd_refined 0.23 r_symmetry_vdw_refined 0.217 r_symmetry_hbond_refined 0.18 r_xyhbond_nbd_refined 0.169 r_chiral_restr 0.167 r_bond_refined_d 0.021 r_gen_planes_refined 0.01 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 917 Nucleic Acid Atoms Solvent Atoms 72 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction ADSC data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing