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Structure of Dps from MICROBACTERIUM ARBORESCENS in the high iron form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1O9R PDB ENTRY 1O9R
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 18% PEG 8000, 2% ISO-PROPANOL, 0.1 M NA-ACETATE, PH 7.5.
Crystal Properties Matthews coefficient Solvent content 2.54 51.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.58 α = 90 b = 92.05 β = 96.04 c = 128.58 γ = 90
Symmetry Space Group P 1 21 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 MARMOSAIC 225 mm CCD M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA SLS X06DA
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 30 98 0.1 7.3 2.05 129605 1.5
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 2.05 96.8 0.88 1.5 2
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 1O9R 2 28.98 129604 6821 100 0.17227 0.16992 0.1784 0.2165 0.2222 RANDOM 31.239
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] -0.95 -0.8 0.89 -0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.545 r_dihedral_angle_3_deg 16.151 r_dihedral_angle_4_deg 11.309 r_dihedral_angle_1_deg 6.557 r_scangle_it 6.166 r_scbond_it 3.721 r_mcangle_it 2.159 r_angle_refined_deg 1.821 r_mcbond_it 1.168 r_chiral_restr 0.138
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.545 r_dihedral_angle_3_deg 16.151 r_dihedral_angle_4_deg 11.309 r_dihedral_angle_1_deg 6.557 r_scangle_it 6.166 r_scbond_it 3.721 r_mcangle_it 2.159 r_angle_refined_deg 1.821 r_mcbond_it 1.168 r_chiral_restr 0.138 r_bond_refined_d 0.025 r_gen_planes_refined 0.009 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 13726 Nucleic Acid Atoms Solvent Atoms 705 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing