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Open and closed forms of wild-type human PRP8 RNase H-like domain with bound Co ion
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ENB PDB entry 3ENB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 298 15% PEG 4000, 300mM MgCl2, 100mM Tris, pH 7.5, vapor diffusion, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.75 55.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.228 α = 90 b = 78.291 β = 90 c = 94.09 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 MARMOSAIC 300 mm CCD 2010-07-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.97949 CLSI 08ID-1
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 1.5 50 88.1 0.067 14.9 3.6 80130 1 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 1.5 1.55 96.3 0.447 2.8 8619
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 3ENB 1.5 34.27 80075 4216 88.01 0.1661 0.1639 0.1641 0.2049 0.2042 RANDOM 22.4173
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] -0.59 0.41 0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.098 r_dihedral_angle_4_deg 16.987 r_dihedral_angle_3_deg 13.447 r_sphericity_free 11.068 r_dihedral_angle_1_deg 5.866 r_scangle_it 5.308 r_sphericity_bonded 4.693 r_scbond_it 4.084 r_mcangle_it 2.915 r_mcbond_it 2.466
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.098 r_dihedral_angle_4_deg 16.987 r_dihedral_angle_3_deg 13.447 r_sphericity_free 11.068 r_dihedral_angle_1_deg 5.866 r_scangle_it 5.308 r_sphericity_bonded 4.693 r_scbond_it 4.084 r_mcangle_it 2.915 r_mcbond_it 2.466 r_rigid_bond_restr 2.045 r_angle_refined_deg 1.814 r_mcbond_other 0.93 r_angle_other_deg 0.885 r_symmetry_vdw_other 0.248 r_nbd_refined 0.235 r_xyhbond_nbd_refined 0.214 r_symmetry_vdw_refined 0.209 r_nbd_other 0.186 r_nbtor_refined 0.182 r_symmetry_hbond_refined 0.16 r_chiral_restr 0.118 r_metal_ion_refined 0.091 r_nbtor_other 0.086 r_bond_refined_d 0.022 r_gen_planes_refined 0.009 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3575 Nucleic Acid Atoms Solvent Atoms 518 Heterogen Atoms 15
Software Software Software Name Purpose SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction CLS data collection DENZO data reduction REFMAC phasing