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Crystal structure of PH domain of ASAP1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DA0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 296 100 mM Na2HPO4, 100 mM Tris, pH 8.0 and 48% PEG400 (v/v)
Crystal Properties Matthews coefficient Solvent content 1.87 34.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.12 α = 90 b = 48.12 β = 90 c = 111.333 γ = 90
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 MARMOSAIC 225 mm CCD 2013-03-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM 1.0 APS 22-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.8 50 95.4 15.6 4.6 22383
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 2DA0 1.8 48.12 21190 1165 95.35 0.21068 0.20801 0.2136 0.25986 0.256 RANDOM 48.008
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] 0.56 0.56 -1.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.239 r_dihedral_angle_3_deg 19.103 r_dihedral_angle_4_deg 17.608 r_long_range_B_refined 8.609 r_long_range_B_other 8.607 r_dihedral_angle_1_deg 7.822 r_scangle_other 5.336 r_mcangle_it 4.331 r_mcangle_other 4.329 r_scbond_it 3.265
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.239 r_dihedral_angle_3_deg 19.103 r_dihedral_angle_4_deg 17.608 r_long_range_B_refined 8.609 r_long_range_B_other 8.607 r_dihedral_angle_1_deg 7.822 r_scangle_other 5.336 r_mcangle_it 4.331 r_mcangle_other 4.329 r_scbond_it 3.265 r_scbond_other 3.259 r_mcbond_other 2.583 r_mcbond_it 2.582 r_angle_refined_deg 1.999 r_angle_other_deg 1.636 r_chiral_restr 0.113 r_bond_refined_d 0.018 r_gen_planes_refined 0.01 r_bond_other_d 0.008 r_gen_planes_other 0.008 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1757 Nucleic Acid Atoms Solvent Atoms 34 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing