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Crystal structure of Deinococcus radiodurans protein DR2400, Pfam domain DUF419
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 298 PEG 3350, Sodium formate 0.2 M, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.2 44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.549 α = 90 b = 82.549 β = 90 c = 35.991 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 298 CCD MARRESEARCH 2005-01-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X9A 0.98 NSLS X9A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.15 20 0.094 0.071 22.6 7.9 7775 7775
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.15 2.23 100 0.48 0.46 4.1 7.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 2.15 20 7418 7418 355 99.97 0.16393 0.161 0.1734 0.22544 0.2316 RANDOM 21.714
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] 0.77 0.39 0.77 -1.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.92 r_dihedral_angle_4_deg 20.878 r_dihedral_angle_3_deg 17.078 r_dihedral_angle_1_deg 6.046 r_scangle_it 3.889 r_scbond_it 2.67 r_angle_refined_deg 1.74 r_mcangle_it 1.578 r_mcbond_it 1.364 r_angle_other_deg 0.897
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.92 r_dihedral_angle_4_deg 20.878 r_dihedral_angle_3_deg 17.078 r_dihedral_angle_1_deg 6.046 r_scangle_it 3.889 r_scbond_it 2.67 r_angle_refined_deg 1.74 r_mcangle_it 1.578 r_mcbond_it 1.364 r_angle_other_deg 0.897 r_symmetry_vdw_other 0.249 r_mcbond_other 0.232 r_nbd_refined 0.207 r_nbd_other 0.196 r_xyhbond_nbd_refined 0.188 r_symmetry_hbond_refined 0.185 r_nbtor_refined 0.172 r_symmetry_vdw_refined 0.169 r_chiral_restr 0.104 r_nbtor_other 0.088 r_bond_refined_d 0.019 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 r_bond_other_d 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1153 Nucleic Acid Atoms Solvent Atoms 111 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MAR345 data collection SCALEPACK data scaling SHELXD phasing SHELXE model building