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Crystal structure of SNX5-PX domain in P212121 space group
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8 277 the protein solution in the final superdex-75 buffer (20 mM Tris.HCl, 100 mM NaCl, 0.02% NaN3, pH 8.0) was concentrated to 8 mg/ml. The Se-Met derivative and the 2.19 A crystals were obtained using an optimized initial crystallization condition of 8 ul of protein vs 1 ul of reservoir solution (0.2M (NH4)2SO4, 0.1M Sodium cacodylate tryhydrate pH 6.5, 30% PEG 8000) at 4C by sitting drop vapor diffusion, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.39 59.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.957 α = 90 b = 75.874 β = 90 c = 77.512 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 RIGAKU SATURN 944 MIRRORS 2006-10-17 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD MARMOSAIC 300 mm CCD ROSENBAUM-ROCK MONOCHROMATOR HIGH-RESOLUTION DOUBLE-CRYSTAL SI(220) SAGITTAL FO
CUSING, ROSENBAUM- ROCK VERTICAL FOCUSING MIRROR 2008-11-18 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 2 SYNCHROTRON APS BEAMLINE 22-ID 0.9793,0.9795,0.9718 APS 22-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 2.19 28.78 93.4 0.033 28.1 4.18 12680 3
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) 2.19 2.27 62.3 0.256 3.5 2.05
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MAD THROUGHOUT 2.19 28.78 11436 1244 93.3 0.24 0.236 0.235 0.284 0.2815 RANDOM 48.12
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] -1.19 0.15 1.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.298 r_dihedral_angle_4_deg 23.943 r_dihedral_angle_3_deg 16.213 r_dihedral_angle_1_deg 5.259 r_scangle_it 3.663 r_scbond_it 2.156 r_mcangle_it 1.324 r_angle_refined_deg 1.284 r_mcbond_it 0.682 r_chiral_restr 0.101
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.298 r_dihedral_angle_4_deg 23.943 r_dihedral_angle_3_deg 16.213 r_dihedral_angle_1_deg 5.259 r_scangle_it 3.663 r_scbond_it 2.156 r_mcangle_it 1.324 r_angle_refined_deg 1.284 r_mcbond_it 0.682 r_chiral_restr 0.101 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1274 Nucleic Acid Atoms Solvent Atoms 135 Heterogen Atoms 1
Software Software Software Name Purpose StructureStudio data collection SnB phasing PHASER phasing REFMAC refinement d*TREK data reduction d*TREK data scaling