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Crystal structure of E. coli DEAD-box protein SrmB bound to regulator of ribonuclease activity A (RraA)
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 7.2 289 CRYSTALS WERE PREPARED USING THE HANGING DROP METHOD AT 16 DEG. C BY MIXING 1:1 PROTEIN SAMPLE WITH MOTHER LIQUOR: 100 MM MAGNESIUM ACETATE, 100 MM MOPS PH 7.2 AND 12% W/V PEG 8000.THE CRYSTALS WERE TRANSFERRED BRIEFLY TO RESERVOIR SOLUTION SUPPLEMENTED WITH 25% (V/V) GLYCEROL AND FLASH FROZEN IN LIQUID NITROGEN.
Crystal Properties Matthews coefficient Solvent content 2.47 50
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.39 α = 90 b = 73.39 β = 90 c = 222.891 γ = 120
Symmetry Space Group P 32 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 2010-01-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 Diamond I04
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 2.9 63.56 99.6 0.12 10.2 4 15208 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 2.9 3.06 99.5 0.51 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 PDB ENTRY 1Q5X 2.9 74.3 15208 804 99.07 0.19544 0.19227 0.1975 0.25658 0.2438 RANDOM 39.431
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] 0.97 0.48 0.97 -1.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.334 r_dihedral_angle_4_deg 21.774 r_dihedral_angle_3_deg 20.397 r_dihedral_angle_1_deg 7.124 r_scangle_it 3.107 r_scbond_it 1.742 r_angle_refined_deg 1.59 r_mcangle_it 1.31 r_mcbond_it 0.674 r_chiral_restr 0.104
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.334 r_dihedral_angle_4_deg 21.774 r_dihedral_angle_3_deg 20.397 r_dihedral_angle_1_deg 7.124 r_scangle_it 3.107 r_scbond_it 1.742 r_angle_refined_deg 1.59 r_mcangle_it 1.31 r_mcbond_it 0.674 r_chiral_restr 0.104 r_bond_refined_d 0.015 r_gen_planes_refined 0.005 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 4964 Nucleic Acid Atoms Solvent Atoms 29 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing