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Crystal structure of the Nup53 RRM domain from Pichia guilliermondii
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1WWH Poly-Ala of 1WWH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.4 294 100mM sodium acetate, 20% PEG 1500, pH 5.4, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.14 42.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.507 α = 90 b = 62.507 β = 90 c = 55.117 γ = 120
Symmetry Space Group P 3 2 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 2010-06-24 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 2.35 38.62 99.8 0.085 21.1 21 5437 59
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) 2.35 2.48 100 0.406 6.5 21.9 782
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-Ala of 1WWH 2.35 20.46 5403 742 99.76 0.2447 0.2379 0.2446 0.2876 0.2315 RANDOM 45.3917
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] -0.18 -0.09 -0.18 0.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.909 r_dihedral_angle_4_deg 20.663 r_dihedral_angle_3_deg 14.846 r_dihedral_angle_1_deg 7.111 r_scangle_it 3.141 r_scbond_it 1.849 r_angle_refined_deg 1.42 r_mcangle_it 1.382 r_angle_other_deg 0.874 r_mcbond_it 0.711
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.909 r_dihedral_angle_4_deg 20.663 r_dihedral_angle_3_deg 14.846 r_dihedral_angle_1_deg 7.111 r_scangle_it 3.141 r_scbond_it 1.849 r_angle_refined_deg 1.42 r_mcangle_it 1.382 r_angle_other_deg 0.874 r_mcbond_it 0.711 r_mcbond_other 0.126 r_chiral_restr 0.074 r_bond_refined_d 0.013 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 668 Nucleic Acid Atoms Solvent Atoms 20 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction SCALA data scaling PHASER phasing