☰ Navigation Tabs
Crystal structure of Staphylococcal nuclease variant Delta+PHS T62A at cryogenic temperature and with high redundancy
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BDC PDB ENTRY 3BDC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 277 21% MPD, 25 mM potassium phosphate, calcium chloride, pdTp, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.2 44.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 31.132 α = 90 b = 60.612 β = 94.04 c = 37.632 γ = 90
Symmetry Space Group P 1 21 1
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 APEX II CCD multilayer 2010-01-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE OTHER
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 1.9 50 99.9 0.0333 22.76 11.42 11069 11067 29.1
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 1.9 1.93 100 0.2658 3.34 4.4 347
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-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 3BDC 1.9 31.91 11069 11067 1092 99.98 0.1684 0.1626 0.2227 0.2126 RANDOM 23.0704
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] -1.52 0.53 -1.25 2.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.516 r_dihedral_angle_3_deg 17.797 r_dihedral_angle_1_deg 6.582 r_dihedral_angle_4_deg 6.49 r_scangle_it 4.399 r_scbond_it 2.993 r_mcangle_it 1.688 r_angle_refined_deg 1.338 r_mcbond_it 1.046 r_chiral_restr 0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.516 r_dihedral_angle_3_deg 17.797 r_dihedral_angle_1_deg 6.582 r_dihedral_angle_4_deg 6.49 r_scangle_it 4.399 r_scbond_it 2.993 r_mcangle_it 1.688 r_angle_refined_deg 1.338 r_mcbond_it 1.046 r_chiral_restr 0.11 r_bond_refined_d 0.012 r_gen_planes_refined 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1031 Nucleic Acid Atoms Solvent Atoms 96 Heterogen Atoms 26
Software Software Software Name Purpose SAINT data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction APEX data collection APEX data reduction