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Crystal structure of RsbX in complex with manganese in space group P1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3W45 PDB ENTRY 3W45
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8.5 298 20 % PEG 1000, 0.1M Tris-HCl, 5mM MgCl2, 3mM MnCl2, pH 8.5, VAPOR DIFFUSION, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.01 38.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 33.198 α = 81.17 b = 41.649 β = 89.96 c = 68.755 γ = 71.46
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 KIRKPATRICK-BAEZ MIRRORS 2009-02-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0000 SPring-8 BL41XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.06 50 90.3 0.081 23.6 3.6 155995 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.06 1.1 71.5 0.366 2.3 2.5
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 3W45 1.06 20 136539 7240 92.18 0.12847 0.12707 0.15492 0.1627 RANDOM 8.484
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] 0.2 -0.26 0.38 -0.01 -0.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.558 r_dihedral_angle_4_deg 16.974 r_dihedral_angle_3_deg 13.783 r_dihedral_angle_1_deg 7.141 r_scangle_it 7.089 r_scbond_it 4.874 r_mcangle_it 3.32 r_mcbond_it 2.266 r_angle_refined_deg 2.216 r_rigid_bond_restr 2.053
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.558 r_dihedral_angle_4_deg 16.974 r_dihedral_angle_3_deg 13.783 r_dihedral_angle_1_deg 7.141 r_scangle_it 7.089 r_scbond_it 4.874 r_mcangle_it 3.32 r_mcbond_it 2.266 r_angle_refined_deg 2.216 r_rigid_bond_restr 2.053 r_angle_other_deg 1.306 r_mcbond_other 0.759 r_chiral_restr 0.161 r_bond_refined_d 0.026 r_gen_planes_refined 0.012 r_gen_planes_other 0.003 r_bond_other_d 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3108 Nucleic Acid Atoms Solvent Atoms 609 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction BSS data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing