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Crystal Structure of N-terminal Domain of Ribosomal Protein L9 (NTL9), G34dA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 291 10 mM Imidazole (pH 8.0), 300 mM Zn Acetate, 3 M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.27 45.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.517 α = 90 b = 53.517 β = 90 c = 36.178 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 2006-06-07 M SINGLE WAVELENGTH
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 1.57 50 99.2 0.062 15.5 9.9 7705 7705
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 1.57 1.63 92.8 0.286 9.3 684
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) 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 Phase from wild type NTL9 THROUGHOUT 1.57 20 7670 7670 355 99.93 0.162 0.162 0.159 0.1717 0.208 0.2308 RANDOM 14.741
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] 0.02 0.02 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.887 r_dihedral_angle_3_deg 12.828 r_sphericity_free 8.58 r_scangle_it 4.461 r_dihedral_angle_1_deg 4.449 r_scbond_it 3.639 r_angle_other_deg 2.871 r_sphericity_bonded 2.454 r_mcangle_it 2.226 r_mcbond_it 1.974
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.887 r_dihedral_angle_3_deg 12.828 r_sphericity_free 8.58 r_scangle_it 4.461 r_dihedral_angle_1_deg 4.449 r_scbond_it 3.639 r_angle_other_deg 2.871 r_sphericity_bonded 2.454 r_mcangle_it 2.226 r_mcbond_it 1.974 r_rigid_bond_restr 1.732 r_angle_refined_deg 1.622 r_mcbond_other 0.568 r_symmetry_hbond_refined 0.392 r_xyhbond_nbd_refined 0.387 r_nbd_refined 0.269 r_metal_ion_refined 0.191 r_nbtor_refined 0.185 r_nbd_other 0.173 r_symmetry_vdw_other 0.142 r_symmetry_vdw_refined 0.108 r_nbtor_other 0.102 r_chiral_restr 0.092 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 400 Nucleic Acid Atoms Solvent Atoms 64 Heterogen Atoms 17
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction REFMAC phasing