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X-ray structure Dps from Kineococcus radiotolerans in complex with Mn (II) ions.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Z90 PDB ENTRY 2Z90
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8 MPD (2-METHYL-2,4-PENTANEDIOL) 45 %, TRIS-HCL 0.1 M, PH 8.0.
Crystal Properties Matthews coefficient Solvent content 2.45 49.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 150.474 α = 90 b = 150.474 β = 90 c = 86.618 γ = 120
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 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 BESSY 14.1
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 50 100 0.08 40.94 16.7 49300 -3 34.7
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 2.07 100 0.34 7.8 14.6
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 PDB ENTRY 2Z90 2 75.24 46797 2491 99.91 0.19608 0.1942 0.2145 0.23226 0.2498 RANDOM 31.07
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] -0.74 -0.37 -0.74 1.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.303 r_dihedral_angle_4_deg 19.35 r_dihedral_angle_3_deg 13.767 r_dihedral_angle_1_deg 4.86 r_scangle_it 1.814 r_scbond_it 1.167 r_angle_refined_deg 1.151 r_mcangle_it 0.595 r_mcbond_it 0.386 r_chiral_restr 0.084
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.303 r_dihedral_angle_4_deg 19.35 r_dihedral_angle_3_deg 13.767 r_dihedral_angle_1_deg 4.86 r_scangle_it 1.814 r_scbond_it 1.167 r_angle_refined_deg 1.151 r_mcangle_it 0.595 r_mcbond_it 0.386 r_chiral_restr 0.084 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 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 5149 Nucleic Acid Atoms Solvent Atoms 305 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing