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Crystal structure of human AND-1 SepB domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4C8S
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 0.1 MHEPES pH 7.0, 1.1M di-sodium malonate and 0.5 % (v/v) Jeffamine ED-2003, supplemented with 0.36 to 0.42 M sulfobetaine NDSB-195
Crystal Properties Matthews coefficient Solvent content 2.89 57.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 249.712 α = 90 b = 249.712 β = 90 c = 249.712 γ = 90
Symmetry Space Group F 4 3 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 6M 2014-08-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.97625 Diamond I02
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rpim I (All) CC (Half) 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 2.503 44.14 99.89 0.1235 0.1274 0.03082 0.999 24.3 16.8 23558 49.66
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.503 2.593 99.52 1.494 1.55 0.4044 0.563 1.92 14.4
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4c8s 2.503 44.14 23555 2155 99.94 0.1781 0.1764 0.1779 0.2107 0.2151
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 10.118 f_angle_d 0.413 f_chiral_restr 0.037 f_plane_restr 0.003 f_bond_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3189 Nucleic Acid Atoms Solvent Atoms 166 Heterogen Atoms 14
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling Aimless data scaling MR-Rosetta phasing