☰ Navigation Tabs
Open and closed forms of T1791P+R1865A human PRP8 RNase H-like domain with bound Mg 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 2.71 54.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.171 α = 90 b = 77.253 β = 90 c = 93.601 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 ADSC QUANTUM 315 2010-01-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.1158 ALS 8.3.1
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 1.95 50 94.3 0.054 13 4 38416 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 1.95 2.02 99.8 0.528 4.1 4005
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 1.95 40.03 38311 2016 93.99 0.1886 0.1865 0.192 0.226 0.233 RANDOM 32.0608
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] -0.06 -0.05 0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.274 r_dihedral_angle_3_deg 14.893 r_dihedral_angle_4_deg 14.465 r_dihedral_angle_1_deg 5.844 r_angle_refined_deg 1.345 r_angle_other_deg 0.761 r_chiral_restr 0.077 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.274 r_dihedral_angle_3_deg 14.893 r_dihedral_angle_4_deg 14.465 r_dihedral_angle_1_deg 5.844 r_angle_refined_deg 1.345 r_angle_other_deg 0.761 r_chiral_restr 0.077 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3490 Nucleic Acid Atoms Solvent Atoms 434 Heterogen Atoms 1
Software Software Software Name Purpose SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction ADSC data collection DENZO data reduction REFMAC phasing