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Crystal Structure of the N-terminal Domain of Ribosomal Protein L9 (NTL9)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 291 10 mM Imidazole (pH 8.0), 200 mM Zn Acetate, 2.5 M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.37 48.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.918 α = 90 b = 53.918 β = 90 c = 36.339 γ = 90
Symmetry Space Group P 41 21 2
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 ADSC QUANTUM 4 2006-03-02 Single wavelenth 2 1 x-ray 1,2 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X26C 1.1 NSLS X26C
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 1.86 50 98.1 0.079 16.4 7.5 4752
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) 1,2 1.86 1.93 85.8 0.345 6 406
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 (All) 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 1.9 20 4526 202 99.6 0.199 0.199 0.197 0.1972 0.236 0.237 RANDOM 20.226
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] -0.04 -0.04 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.275 r_dihedral_angle_3_deg 16.258 r_scangle_it 5.797 r_dihedral_angle_1_deg 4.636 r_scbond_it 3.29 r_mcangle_it 1.915 r_angle_refined_deg 1.509 r_mcbond_it 1.151 r_xyhbond_nbd_refined 0.394 r_symmetry_hbond_refined 0.353
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.275 r_dihedral_angle_3_deg 16.258 r_scangle_it 5.797 r_dihedral_angle_1_deg 4.636 r_scbond_it 3.29 r_mcangle_it 1.915 r_angle_refined_deg 1.509 r_mcbond_it 1.151 r_xyhbond_nbd_refined 0.394 r_symmetry_hbond_refined 0.353 r_nbtor_refined 0.313 r_nbd_refined 0.221 r_symmetry_vdw_refined 0.205 r_chiral_restr 0.096 r_symmetry_metal_ion_refined 0.081 r_metal_ion_refined 0.06 r_bond_refined_d 0.015 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 390 Nucleic Acid Atoms Solvent Atoms 52 Heterogen Atoms 4
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction ADSC data collection