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Crystal structure of the RrgA Jo.In complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2WW8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 1 uL of protein (23 mg/ml in 50 mM Tris pH 8.0, 150 mM NaCl) and 1 uL of reservoir (2 M ammonium sulfate, 4% isopropanol
Crystal Properties Matthews coefficient Solvent content 2.2252 40
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 132.541 α = 90 b = 134.571 β = 90 c = 144.474 γ = 90
Symmetry Space Group P 21 21 21
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 MARMOSAIC 225 mm CCD 2010-11-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.87260 ESRF ID23-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 2.04 45.91 93.6 0.046 1 30.6 4.6 153725 -3 3 41.71
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.04 2.17 83.8 0.549 0.883 3.02 4.6
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 2WW8 2.04 45.9 149827 3898 93.96 0.21401 0.21324 0.2247 0.24309 0.2563 RANDOM 53.728
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] -1.56 -1.79 3.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.284 r_dihedral_angle_4_deg 18.043 r_dihedral_angle_3_deg 13.502 r_long_range_B_other 10.033 r_long_range_B_refined 10.026 r_dihedral_angle_1_deg 7.883 r_scangle_other 7.448 r_scbond_it 5.801 r_scbond_other 5.163 r_mcangle_it 4.949
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.284 r_dihedral_angle_4_deg 18.043 r_dihedral_angle_3_deg 13.502 r_long_range_B_other 10.033 r_long_range_B_refined 10.026 r_dihedral_angle_1_deg 7.883 r_scangle_other 7.448 r_scbond_it 5.801 r_scbond_other 5.163 r_mcangle_it 4.949 r_mcangle_other 4.949 r_mcbond_it 3.679 r_mcbond_other 3.672 r_angle_refined_deg 1.266 r_angle_other_deg 0.63 r_chiral_restr 0.084 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9802 Nucleic Acid Atoms Solvent Atoms 1023 Heterogen Atoms 81
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing