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Crystal structure of the ArfGAP domain of human ARFGAP1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GF9 pdb entry 2gf9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 291 3.5M Sodium Formate, 0.1M Tris, 1:100 chymotrypsin, pH 8.5, vapor diffusion, sitting drop, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.36 47.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.422 α = 90 b = 82.422 β = 90 c = 81.008 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 315 2008-07-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97935 APS 19-ID
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 2.4 50 99.6 0.092 8.1 7.4 12298
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 2.4 2.44 98.3 0.653 6.5 591
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT pdb entry 2gf9 2.4 30 12266 588 99.537 0.236 0.234 0.273 0.2876 thin shells 21.648
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] -2.321 -1.16 -2.321 3.481
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.521 r_dihedral_angle_4_deg 21.775 r_dihedral_angle_3_deg 15.087 r_dihedral_angle_1_deg 6.217 r_scangle_it 2.181 r_mcangle_it 2.025 r_scbond_it 1.536 r_angle_refined_deg 1.445 r_mcbond_it 1.309 r_angle_other_deg 0.924
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.521 r_dihedral_angle_4_deg 21.775 r_dihedral_angle_3_deg 15.087 r_dihedral_angle_1_deg 6.217 r_scangle_it 2.181 r_mcangle_it 2.025 r_scbond_it 1.536 r_angle_refined_deg 1.445 r_mcbond_it 1.309 r_angle_other_deg 0.924 r_mcbond_other 0.324 r_chiral_restr 0.073 r_bond_refined_d 0.017 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1757 Nucleic Acid Atoms Solvent Atoms 11 Heterogen Atoms 4
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction DM phasing MolProbity model building Coot model building