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Methanopyrus Kandleri FEN-1 nuclease
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RXW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 290 PEG4000, Tris-HCL, sodium chloride, calcium chloride
Crystal Properties Matthews coefficient Solvent content 2.18 43.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.331 α = 90 b = 86.193 β = 90 c = 147.617 γ = 90
Symmetry Space Group P 21 21 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 ADSC QUANTUM 315r 2010-04-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.97946 SSRL BL9-2
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 2.2 74.43 96.4 0.088 10.6 5.9 35363 39.2
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 2.2 2.26 88.5 0.741 2.2 5.9
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 MOLECULAR REPLACEMENT THROUGHOUT 1RXW 2.2 74.43 33535 1758 96.24 0.20165 0.20011 0.2088 0.23134 0.2375 RANDOM 53.506
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] 2.78 -0.8 -1.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.983 r_dihedral_angle_4_deg 16.431 r_dihedral_angle_3_deg 12.677 r_dihedral_angle_1_deg 5.508 r_long_range_B_refined 5.015 r_long_range_B_other 5.008 r_scangle_other 3.329 r_mcangle_it 2.367 r_mcangle_other 2.366 r_scbond_it 2.036
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.983 r_dihedral_angle_4_deg 16.431 r_dihedral_angle_3_deg 12.677 r_dihedral_angle_1_deg 5.508 r_long_range_B_refined 5.015 r_long_range_B_other 5.008 r_scangle_other 3.329 r_mcangle_it 2.367 r_mcangle_other 2.366 r_scbond_it 2.036 r_scbond_other 2.036 r_mcbond_it 1.469 r_mcbond_other 1.469 r_angle_refined_deg 1.194 r_angle_other_deg 0.879 r_chiral_restr 0.065 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.003 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4752 Nucleic Acid Atoms Solvent Atoms 86 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement PHASER phasing