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Crystal structure of protein with unknown function from Deinococcus radiodurans at P61 spacegroup
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3E8O
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 293 0.5M Sodium chloride, 10mM HEPES, 0.1M Sodium acetate, 2.6M Ammonium sulfate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.36 47.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.39 α = 90 b = 80.39 β = 90 c = 69.92 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 MAR CCD 165 mm GRAPHITE 2011-03-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON KURCHATOV SNC BEAMLINE K4.4 0.9815 KURCHATOV SNC K4.4
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.47 20 98 44067 43293 -3 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.47 1.55 97.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 3E8O 1.47 19.37 67760 41305 2181 99.57 0.15094 0.14969 0.153 0.17462 0.1783 RANDOM 19.6
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] 3.34 3.34 -6.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.712 r_dihedral_angle_4_deg 24.718 r_dihedral_angle_3_deg 12.411 r_long_range_B_refined 6.213 r_long_range_B_other 6.211 r_dihedral_angle_1_deg 5.72 r_scangle_other 4.216 r_scbond_it 2.852 r_scbond_other 2.85 r_angle_other_deg 2.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.712 r_dihedral_angle_4_deg 24.718 r_dihedral_angle_3_deg 12.411 r_long_range_B_refined 6.213 r_long_range_B_other 6.211 r_dihedral_angle_1_deg 5.72 r_scangle_other 4.216 r_scbond_it 2.852 r_scbond_other 2.85 r_angle_other_deg 2.27 r_mcangle_it 2.186 r_mcangle_other 2.186 r_angle_refined_deg 1.901 r_mcbond_it 1.519 r_mcbond_other 1.519 r_chiral_restr 0.116 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1571 Nucleic Acid Atoms Solvent Atoms 241 Heterogen Atoms 29
Software Software Software Name Purpose MAR345dtb data collection MOLREP phasing REFMAC refinement XDS data reduction XSCALE data scaling