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Crystal structure of Sulfolobus solfataricus Nop5 (1-262) and fibrillarin complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2NNW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.2 293 20% PEG 3350, 0.2M KF, pH 7.2, vapor diffusion, hanging drop, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.37 48.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.517 α = 90 b = 182.364 β = 90 c = 79.14 γ = 90
Symmetry Space Group C 2 2 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 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0000 SPring-8 BL41XU
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 2.6 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 2NNW 2.6 20 17155 876 99.88 0.235 0.232 0.2285 0.285 0.2803 RANDOM 32.101
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] 2.9 0.09 -2.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.921 r_dihedral_angle_3_deg 21.619 r_dihedral_angle_4_deg 19.889 r_dihedral_angle_1_deg 6.001 r_scangle_it 1.733 r_angle_refined_deg 1.307 r_scbond_it 1.064 r_mcangle_it 0.703 r_mcbond_it 0.405 r_nbtor_refined 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.921 r_dihedral_angle_3_deg 21.619 r_dihedral_angle_4_deg 19.889 r_dihedral_angle_1_deg 6.001 r_scangle_it 1.733 r_angle_refined_deg 1.307 r_scbond_it 1.064 r_mcangle_it 0.703 r_mcbond_it 0.405 r_nbtor_refined 0.308 r_symmetry_hbond_refined 0.282 r_nbd_refined 0.213 r_symmetry_vdw_refined 0.213 r_xyhbond_nbd_refined 0.147 r_chiral_restr 0.096 r_bond_refined_d 0.01 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3881 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling PHASER phasing