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Crystal structure of E. coli regulator of ribonuclease activity A (RraA) bound to fragment of DEAD-box protein RhlB
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Q5X PDB ENTRY 1Q5X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.4 298 CRYSTALS WERE OBTAINED USING THE HANGING DROP METHOD, BY MIXING IN 1 TO 1 RATIO PROTEIN SAMPLE WITH MOTHER LIQUOR 100 MM SODIUM CITRATE PH 5.4, 32% MPD AND 200 MM AMMONIUM ACETATE AT 25 C. PLATES WERE THEN IMMEDIATELY TRANSFERRED TO 16 C. CRYSTALS WERE DIRECTLY FLASH FROZEN IN LIQUID NITROGEN.
Crystal Properties Matthews coefficient Solvent content 2.58 52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 259.63 α = 90 b = 69.07 β = 109.17 c = 123.3 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 ADSC CCD MIRRORS 2010-03-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 Diamond I02
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 2.8 63.53 98 0.05 15.5 2.9 47500 6
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 2.8 2.95 99.3 0.26 3.7 2.9
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1Q5X 2.8 122.62 47500 2535 97.52 0.22434 0.22087 0.28774 0.2924 RANDOM 57.396
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] 0.15 1.25 2.63 -1.96
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.472 r_dihedral_angle_3_deg 19.141 r_dihedral_angle_4_deg 18.07 r_dihedral_angle_1_deg 6.619 r_scangle_it 3.003 r_scbond_it 1.647 r_angle_refined_deg 1.507 r_mcangle_it 1.226 r_mcbond_it 0.695 r_chiral_restr 0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.472 r_dihedral_angle_3_deg 19.141 r_dihedral_angle_4_deg 18.07 r_dihedral_angle_1_deg 6.619 r_scangle_it 3.003 r_scbond_it 1.647 r_angle_refined_deg 1.507 r_mcangle_it 1.226 r_mcbond_it 0.695 r_chiral_restr 0.1 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14380 Nucleic Acid Atoms Solvent Atoms 65 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing