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Crystal structure of cell-death related nuclease 4 (CRN-4) bound with Er
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3CG7 PDB ENTRY 3CG7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 277 0.2M sodium formate, 20% PEG 3350, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 4.71 73.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 130.279 α = 90 b = 157.795 β = 90 c = 65.244 γ = 90
Symmetry Space Group P 21 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 315 2007-07-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL13B1 0.999 NSRRC BL13B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 30 99.8 0.077 19.6 4.9 43224 43082 3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.6 2.69 100 0.436 5.1 4240
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (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 3CG7 2.6 30 42080 39961 2119 99.76 0.22484 0.2243 0.26516 0.2639 RANDOM 41.791
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] -2.05 2.61 -0.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.501 r_dihedral_angle_3_deg 18.327 r_dihedral_angle_4_deg 16.327 r_dihedral_angle_1_deg 6.147 r_scangle_it 2.7 r_scbond_it 1.697 r_angle_refined_deg 1.32 r_mcangle_it 1.273 r_mcbond_it 0.725 r_nbtor_refined 0.314
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.501 r_dihedral_angle_3_deg 18.327 r_dihedral_angle_4_deg 16.327 r_dihedral_angle_1_deg 6.147 r_scangle_it 2.7 r_scbond_it 1.697 r_angle_refined_deg 1.32 r_mcangle_it 1.273 r_mcbond_it 0.725 r_nbtor_refined 0.314 r_nbd_refined 0.215 r_symmetry_vdw_refined 0.179 r_xyhbond_nbd_refined 0.169 r_symmetry_hbond_refined 0.166 r_chiral_restr 0.102 r_bond_refined_d 0.012 r_gen_planes_refined 0.004 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4806 Nucleic Acid Atoms Solvent Atoms 154 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling AMoRE phasing