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Exonuclease domain-containing 1 (Exd1) in the native conformation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5FIS PDB ENTRY 5FIS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 35% (W/V) 1,6-HEXANEDIOL, 50 MM TRIS-HCL PH 8.5, 5 MM MGSO4
Crystal Properties Matthews coefficient Solvent content 2.58 52.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 122.54 α = 90 b = 81.58 β = 111.1 c = 154.75 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 PIXEL DECTRIS PILATUS 6M TOROIDAL MIRROR 2014-04-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 ESRF ID29
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 2.4 50 96 0.15 6.6 3.8 53690 1
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 2.4 2.5 85.8 0.97 1.3 3.4
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 PDB ENTRY 5FIS 2.4 50.01 51094 2596 96.06 0.22226 0.221 0.2237 0.24717 0.2513 RANDOM 60.371
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] -0.16 0.51 -3.16 2.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.262 r_dihedral_angle_3_deg 19.378 r_dihedral_angle_4_deg 15.115 r_dihedral_angle_1_deg 6.502 r_mcangle_it 2.82 r_scbond_it 2.106 r_angle_refined_deg 2.012 r_mcbond_it 1.659 r_mcbond_other 1.658 r_angle_other_deg 1.569
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.262 r_dihedral_angle_3_deg 19.378 r_dihedral_angle_4_deg 15.115 r_dihedral_angle_1_deg 6.502 r_mcangle_it 2.82 r_scbond_it 2.106 r_angle_refined_deg 2.012 r_mcbond_it 1.659 r_mcbond_other 1.658 r_angle_other_deg 1.569 r_chiral_restr 0.113 r_bond_refined_d 0.02 r_gen_planes_refined 0.012 r_bond_other_d 0.01 r_gen_planes_other 0.007 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_mcangle_other r_scbond_other r_scangle_it 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 9685 Nucleic Acid Atoms Solvent Atoms 53 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing