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crystal structure of porcine RNase 4 D80A mutant in complex with dCMP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5ARJ PDB ENTRY 5ARJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.6 0.1 M SODIUM CITRATE PH 5.6, 20 % (V/V) 2-PROPANOL, 20 % (W/V) PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.11 41.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 30.962 α = 89.78 b = 62.515 β = 79.21 c = 70.216 γ = 78.9
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 2014-08-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 Diamond I02
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 29.5 91.5 0.1 27 3.1 14168 6
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 2.72 65.6 0.41 10.7 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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 5ARJ 2.61 68.94 13322 723 90.78 0.25486 0.25232 0.2562 0.29958 0.3015 RANDOM 46.109
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] -2.89 -2.15 -2.18 0.48 4 0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.156 r_dihedral_angle_3_deg 15.541 r_dihedral_angle_4_deg 13.32 r_dihedral_angle_1_deg 7.082 r_mcangle_it 5.823 r_scbond_it 4.116 r_mcbond_it 3.669 r_mcbond_other 3.669 r_angle_refined_deg 1.514 r_angle_other_deg 1.136
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.156 r_dihedral_angle_3_deg 15.541 r_dihedral_angle_4_deg 13.32 r_dihedral_angle_1_deg 7.082 r_mcangle_it 5.823 r_scbond_it 4.116 r_mcbond_it 3.669 r_mcbond_other 3.669 r_angle_refined_deg 1.514 r_angle_other_deg 1.136 r_chiral_restr 0.078 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.006 r_gen_planes_other 0.005 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 3864 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 80
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing