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X-ray Structure of RbmB from Streptomyces ribosidificus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2C7T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 24-26% PEG-3350, 100 mM MgCl2, 100 mM MOPS, 1 mM PLP, 5 mM 2-DOS
Crystal Properties Matthews coefficient Solvent content 2.16 42.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.072 α = 90 b = 101.072 β = 90 c = 160.004 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 Bruker Platinum 135 montel 2017-02-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.1 50 99.2 0.092 0.092 10.3 8.3 48736
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.2 98.2 0.375 0.375 2.8 4.1
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 2c7t 2.1 50 46279 2457 99.3 0.18497 0.18236 0.1939 0.23322 0.2427 RANDOM 20.551
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] -1.36 -1.36 2.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.209 r_dihedral_angle_4_deg 20.587 r_dihedral_angle_3_deg 17.188 r_dihedral_angle_1_deg 6.778 r_long_range_B_refined 4.791 r_long_range_B_other 4.739 r_scangle_other 3.731 r_scbond_it 2.443 r_scbond_other 2.443 r_mcangle_it 2.408
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.209 r_dihedral_angle_4_deg 20.587 r_dihedral_angle_3_deg 17.188 r_dihedral_angle_1_deg 6.778 r_long_range_B_refined 4.791 r_long_range_B_other 4.739 r_scangle_other 3.731 r_scbond_it 2.443 r_scbond_other 2.443 r_mcangle_it 2.408 r_mcangle_other 2.408 r_angle_refined_deg 2.083 r_mcbond_it 1.618 r_mcbond_other 1.617 r_angle_other_deg 1.223 r_chiral_restr 0.118 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6174 Nucleic Acid Atoms Solvent Atoms 342 Heterogen Atoms 56
Software Software Software Name Purpose REFMAC refinement SAINT data reduction SADABS data scaling PHASER phasing