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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: manganese
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 = 55.009 α = 90 b = 55.009 β = 90 c = 109.025 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 1.5 30 98.4 50076 50076 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 1.5 1.54 99
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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 1.5 15 2 25612 25612 1358 98.43 0.17 0.16761 0.16672 0.18456 RANDOM 24.806
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] 0.37 0.37 -0.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.063 r_dihedral_angle_4_deg 20.078 r_dihedral_angle_3_deg 12.365 r_sphericity_free 7.469 r_scangle_it 5.941 r_sphericity_bonded 5.255 r_dihedral_angle_1_deg 5.028 r_scbond_it 4.082 r_mcangle_it 2.574 r_rigid_bond_restr 2.397
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.063 r_dihedral_angle_4_deg 20.078 r_dihedral_angle_3_deg 12.365 r_sphericity_free 7.469 r_scangle_it 5.941 r_sphericity_bonded 5.255 r_dihedral_angle_1_deg 5.028 r_scbond_it 4.082 r_mcangle_it 2.574 r_rigid_bond_restr 2.397 r_mcbond_it 1.877 r_angle_refined_deg 1.456 r_nbtor_refined 0.315 r_nbd_refined 0.198 r_symmetry_vdw_refined 0.191 r_symmetry_hbond_refined 0.162 r_xyhbond_nbd_refined 0.161 r_chiral_restr 0.091 r_bond_refined_d 0.013 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 738 Nucleic Acid Atoms Solvent Atoms 132 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling CNS phasing