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Crystal structure of the C-terminal domain of nuclear pore complex component NUP116 from Candida glabrata
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3KEP Poly-alanine model of yeast Nup145 PDB ID: 3KEP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.2 294 100mM MES, 25% PEGMME 2000, 200mM Sodium potassium tartarae, 0.4microL of 5% ethylacetate used additive into 2microL drop, pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.35 47.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.703 α = 90 b = 67.668 β = 101.37 c = 55.119 γ = 90
Symmetry Space Group P 1 21 1
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 RAYONIX MX225HE 2010-02-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.97929 APS 31-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.94 34.37 99.5 0.14 8.3 7 25957 20
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.94 2.04 99.6 0.471 3.6 6.9
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 Poly-alanine model of yeast Nup145 PDB ID: 3KEP 1.94 25.09 24613 1318 100 0.20924 0.20666 0.2179 0.25617 0.2669 RANDOM 22.325
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] 0.01 -0.01 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.464 r_dihedral_angle_4_deg 13.551 r_dihedral_angle_3_deg 13.318 r_dihedral_angle_1_deg 6.275 r_scangle_it 4.504 r_scbond_it 2.926 r_mcangle_it 1.998 r_angle_refined_deg 1.781 r_mcbond_it 1.117 r_angle_other_deg 1.015
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.464 r_dihedral_angle_4_deg 13.551 r_dihedral_angle_3_deg 13.318 r_dihedral_angle_1_deg 6.275 r_scangle_it 4.504 r_scbond_it 2.926 r_mcangle_it 1.998 r_angle_refined_deg 1.781 r_mcbond_it 1.117 r_angle_other_deg 1.015 r_mcbond_other 0.301 r_chiral_restr 0.11 r_bond_refined_d 0.02 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2394 Nucleic Acid Atoms Solvent Atoms 150 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction SCALA data scaling PHASER phasing