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Crystal structure of the GIY-YIG N-terminal endonuclease domain of UvrC from Bacillus caldotenax
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.4 295 Ammonium Sulfate, DTT, Sodium Acetate, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.4 49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.487 α = 90 b = 86.66 β = 120.16 c = 67.862 γ = 90
Symmetry Space Group C 1 2 1
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 2003-01-01 M MAD 2 1 3 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X26C 1.0 NSLS X26C 2 SYNCHROTRON NSLS BEAMLINE X12B 1.0 NSLS X12B 3 SYNCHROTRON NSLS BEAMLINE X25 1.0 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 2 30 100 29029 29029 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) 2 2.08 100
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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT 2 15 2 27724 27724 1487 100 0.219 0.20496 0.2024 0.2112 0.25203 0.258 RANDOM 36.111
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] -0.43 -2.24 0.83 -2.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.154 r_dihedral_angle_4_deg 17.4 r_dihedral_angle_3_deg 15.875 r_dihedral_angle_1_deg 5.218 r_scangle_it 3.383 r_scbond_it 2.303 r_mcangle_it 1.675 r_angle_refined_deg 1.508 r_mcbond_it 1.062 r_angle_other_deg 0.869
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.154 r_dihedral_angle_4_deg 17.4 r_dihedral_angle_3_deg 15.875 r_dihedral_angle_1_deg 5.218 r_scangle_it 3.383 r_scbond_it 2.303 r_mcangle_it 1.675 r_angle_refined_deg 1.508 r_mcbond_it 1.062 r_angle_other_deg 0.869 r_symmetry_vdw_refined 0.217 r_nbd_refined 0.212 r_mcbond_other 0.21 r_symmetry_vdw_other 0.207 r_nbd_other 0.183 r_xyhbond_nbd_refined 0.18 r_nbtor_refined 0.177 r_symmetry_hbond_refined 0.151 r_chiral_restr 0.107 r_nbtor_other 0.089 r_bond_refined_d 0.015 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 2966 Nucleic Acid Atoms Solvent Atoms 126 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling SOLVE phasing