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crystal structure of a repair endonuclease from Pyrococcus abyssi
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 pH 7
Crystal Properties Matthews coefficient Solvent content 2.76 55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.966 α = 90 b = 100.688 β = 90 c = 157.686 γ = 90
Symmetry Space Group C 2 2 21
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 MARRESEARCH 2006-06-22 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 ESRF BM14
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 2.6 25 99 0.05 37.3 4.6 19639 2
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 2.6 2.7 99.4 0.41 2.9 3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 NONE 2.6 10 18306 996 99.9 0.243 0.243 0.2318 0.248 0.2393 RANDOM 66.65
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] 8.38 -5.97 -2.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.815 r_dihedral_angle_4_deg 21.369 r_dihedral_angle_3_deg 20.302 r_dihedral_angle_1_deg 7.896 r_scangle_it 3.889 r_scbond_it 2.431 r_mcangle_it 1.963 r_angle_refined_deg 1.462 r_mcbond_it 1.2 r_symmetry_vdw_refined 0.399
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.815 r_dihedral_angle_4_deg 21.369 r_dihedral_angle_3_deg 20.302 r_dihedral_angle_1_deg 7.896 r_scangle_it 3.889 r_scbond_it 2.431 r_mcangle_it 1.963 r_angle_refined_deg 1.462 r_mcbond_it 1.2 r_symmetry_vdw_refined 0.399 r_nbtor_refined 0.313 r_symmetry_hbond_refined 0.244 r_nbd_refined 0.231 r_xyhbond_nbd_refined 0.145 r_chiral_restr 0.099 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3679 Nucleic Acid Atoms Solvent Atoms 112 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling CNS phasing