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Crystal structure of the GIY-YIG N-terminal endonuclease domain of UvrC from Thermotoga maritima bound to its catalytic divalent cation: magnesium
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 295 PEG 8000, Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 3.7 66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.246 α = 90 b = 55.246 β = 90 c = 108.63 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 2004-01-01 M SINGLE WAVELENGTH 2 1 3 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X26C 1.1 NSLS X26C 2 SYNCHROTRON NSLS BEAMLINE X12B 1.1 NSLS X12B 3 SYNCHROTRON NSLS BEAMLINE X25 1.1 NSLS X25
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 1.8 30 99.7 16305 16305 2 2
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 1.8 1.86 100
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 1.8 15 2 15386 15386 830 99.78 0.18 0.17647 0.17518 0.1887 0.20198 RANDOM 21.77
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] 0.26 0.26 -0.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.169 r_dihedral_angle_4_deg 16.922 r_dihedral_angle_3_deg 14.126 r_dihedral_angle_1_deg 5.154 r_scangle_it 5.135 r_scbond_it 3.487 r_mcangle_it 1.641 r_mcbond_it 1.585 r_angle_refined_deg 1.473 r_symmetry_metal_ion_refined 1.112
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.169 r_dihedral_angle_4_deg 16.922 r_dihedral_angle_3_deg 14.126 r_dihedral_angle_1_deg 5.154 r_scangle_it 5.135 r_scbond_it 3.487 r_mcangle_it 1.641 r_mcbond_it 1.585 r_angle_refined_deg 1.473 r_symmetry_metal_ion_refined 1.112 r_angle_other_deg 0.821 r_symmetry_vdw_other 0.306 r_mcbond_other 0.292 r_nbd_refined 0.226 r_nbtor_refined 0.182 r_nbd_other 0.173 r_symmetry_hbond_refined 0.128 r_symmetry_vdw_refined 0.113 r_xyhbond_nbd_refined 0.112 r_nbtor_other 0.084 r_chiral_restr 0.083 r_bond_refined_d 0.017 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 738 Nucleic Acid Atoms Solvent Atoms 96 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling CNS phasing