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Crystal structure of Sulfolobus solfataricus Nop5 (135-380)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2NNW PDB entry 2NNW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.7 293 0.8M (NH4)2SO4, 10 mM MgCl2, and 50mM Na cacodylate, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.7 66.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 153.645 α = 90 b = 122.126 β = 107.67 c = 71.786 γ = 90
Symmetry Space Group C 1 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 MAR CCD 165 mm SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BSRF BEAMLINE 3W1A 0.9800 BSRF 3W1A
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 3.1 50 99.4 0.149 10.5 3.9 22817
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) 1 3.1 3.21 99.1 0.475 2.6 3.9
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 PDB entry 2NNW 3.1 20 22738 1169 99.06 0.263 0.261 0.2592 0.304 0.3027 RANDOM 23.468
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] 0.93 -0.67 -1.66 0.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.259 r_dihedral_angle_3_deg 21.167 r_dihedral_angle_4_deg 19.289 r_dihedral_angle_1_deg 4.641 r_scangle_it 1.469 r_angle_refined_deg 1.154 r_scbond_it 0.818 r_mcangle_it 0.541 r_mcbond_it 0.316 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.259 r_dihedral_angle_3_deg 21.167 r_dihedral_angle_4_deg 19.289 r_dihedral_angle_1_deg 4.641 r_scangle_it 1.469 r_angle_refined_deg 1.154 r_scbond_it 0.818 r_mcangle_it 0.541 r_mcbond_it 0.316 r_nbtor_refined 0.305 r_symmetry_vdw_refined 0.242 r_nbd_refined 0.22 r_xyhbond_nbd_refined 0.135 r_chiral_restr 0.081 r_symmetry_hbond_refined 0.039 r_bond_refined_d 0.01 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5361 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 25
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction MAR345 data collection