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Crystal structure of mitochondrial 5'(3')-deoxy ribonucleotidase alternative spliced variant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4L6A PDB ENTRY 4L6A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4 291 20 mM potassium phosphate monobasic, 8% PEG8000, 10% gycerol, pH 4, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 3.01 59.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.372 α = 90 b = 73.372 β = 90 c = 106.672 γ = 90
Symmetry Space Group P 43 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 RAYONIX MX-225 2012-01-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.97826 BESSY 14.2
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 1.271 46.656 98.8 0.036 26.48 76192 -3 19.812
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 1.271 1.35 92.7 0.608 2.05
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 4L6A 1.271 46.656 76191 3809 98.8 0.1321 0.1312 0.1492 0.1559 RANDOM 18.6249
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] 0.33 0.33 -0.65
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 28.047 r_dihedral_angle_2_deg 27.745 r_dihedral_angle_4_deg 16.742 r_dihedral_angle_3_deg 11.423 r_sphericity_bonded 8.708 r_rigid_bond_restr 7.619 r_dihedral_angle_1_deg 6.01 r_angle_refined_deg 2.336 r_angle_other_deg 2.077 r_mcangle_it 1.124
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 28.047 r_dihedral_angle_2_deg 27.745 r_dihedral_angle_4_deg 16.742 r_dihedral_angle_3_deg 11.423 r_sphericity_bonded 8.708 r_rigid_bond_restr 7.619 r_dihedral_angle_1_deg 6.01 r_angle_refined_deg 2.336 r_angle_other_deg 2.077 r_mcangle_it 1.124 r_mcbond_other 0.797 r_mcbond_it 0.796 r_chiral_restr 0.143 r_bond_refined_d 0.02 r_gen_planes_refined 0.012 r_gen_planes_other 0.011 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1607 Nucleic Acid Atoms Solvent Atoms 288 Heterogen Atoms 77
Software Software Software Name Purpose XSCALE data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XDS data scaling