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Crystal structure of a duf162 family protein (dr_1909) from deinococcus radiodurans at 1.70 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP, NANODROP 8.3 277 20.0% PEG-3350, 0.2M K3Citrate, No Buffer, pH 8.3, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K 2 VAPOR DIFFUSION, SITTING DROP, NANODROP 7.5 277 0.2M MgCl2, 30.0% PEG-400, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.41 α = 90 b = 53.41 β = 90 c = 118.31 γ = 90
Symmetry Space Group P 43 21 2
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 ADSC QUANTUM 4 2004-08-26 M SINGLE WAVELENGTH 2 2 x-ray 100 CCD ADSC QUANTUM 315 1m long Rh coated bent cylindrical mirror for horizontal and vertical focusing 2006-01-12 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.3 ALS 5.0.3 2 SYNCHROTRON SSRL BEAMLINE BL1-5 0.918381, 0.979310, 0.978359 SSRL BL1-5
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 1.7 27.28 98.3 0.067 18.38 19674 25.34
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 1.7 1.76 94.7 0.498 2.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MAD THROUGHOUT 1.7 27.28 19611 984 99.79 0.18 0.178 0.1856 0.22 0.216 RANDOM 19.501
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] -0.28 -0.28 0.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.646 r_dihedral_angle_4_deg 19.185 r_dihedral_angle_3_deg 10.805 r_dihedral_angle_1_deg 6.218 r_scangle_it 5.939 r_scbond_it 4.089 r_mcangle_it 2.317 r_mcbond_it 1.716 r_angle_refined_deg 1.344 r_angle_other_deg 0.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.646 r_dihedral_angle_4_deg 19.185 r_dihedral_angle_3_deg 10.805 r_dihedral_angle_1_deg 6.218 r_scangle_it 5.939 r_scbond_it 4.089 r_mcangle_it 2.317 r_mcbond_it 1.716 r_angle_refined_deg 1.344 r_angle_other_deg 0.78 r_mcbond_other 0.434 r_symmetry_vdw_other 0.246 r_nbd_refined 0.211 r_nbd_other 0.185 r_symmetry_hbond_refined 0.177 r_nbtor_refined 0.169 r_xyhbond_nbd_refined 0.147 r_nbtor_other 0.081 r_symmetry_vdw_refined 0.079 r_chiral_restr 0.074 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1216 Nucleic Acid Atoms Solvent Atoms 132 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction SHARP phasing