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Structure of a Rom protein dimer at 1.55 angstrom resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ROP PDB entry 1ROP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 Hanging drop contained 1 uL protein/RNA mixture (0.3 0.4 mM complex) and 1 uL well buffer (50 mM sodium cacodylate pH 6.0, 0.1 M potassium chloride, 25 mM magnesium chloride, and 15% isopropanol)., VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 1.82 32.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.391 α = 90 b = 39.364 β = 95.89 c = 27.1 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 105 IMAGE PLATE RIGAKU RAXIS IV Blue Max-flux confocal mirrors 2006-07-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
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 1.55 100 94.8 0.072 11.1 14338 3 3
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 1.55 1.61 60.6 0.244 2.7 913
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 1ROP 1.55 48.91 13607 729 94.78 0.17181 0.16942 0.1642 0.21616 0.2161 RANDOM 16.462
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] 0.35 0.07 -0.34 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.668 r_dihedral_angle_4_deg 23.05 r_dihedral_angle_3_deg 14.17 r_sphericity_free 4.819 r_scangle_it 4.794 r_dihedral_angle_1_deg 4.304 r_scbond_it 3.335 r_sphericity_bonded 3.241 r_mcangle_it 2.105 r_rigid_bond_restr 1.937
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.668 r_dihedral_angle_4_deg 23.05 r_dihedral_angle_3_deg 14.17 r_sphericity_free 4.819 r_scangle_it 4.794 r_dihedral_angle_1_deg 4.304 r_scbond_it 3.335 r_sphericity_bonded 3.241 r_mcangle_it 2.105 r_rigid_bond_restr 1.937 r_mcbond_it 1.455 r_angle_refined_deg 1.387 r_nbtor_refined 0.302 r_symmetry_vdw_refined 0.256 r_nbd_refined 0.23 r_xyhbond_nbd_refined 0.216 r_symmetry_hbond_refined 0.192 r_chiral_restr 0.1 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 912 Nucleic Acid Atoms Solvent Atoms 165 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection d*TREK data reduction d*TREK data scaling PHASER phasing