☰ Navigation Tabs
Crystal structure of Staphylococcal nuclease variant Delta+PHS I92KL25A at cryogenic temperature
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 9 277 27% MPD, 25 mM potassium phosphate, 4.5 mg/mL (0.28 mM) protein, 0.84 mM calcium chloride, 0.56 mM pdTp, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.2 44.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 31.061 α = 90 b = 59.875 β = 94.91 c = 38.269 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 ADSC QUANTUM 315 2010-01-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 NSLS X25
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 1.63 50 98.9 0.048 16.5 6 17261 17261 31.1
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 1.63 1.66 87 0.281 4.6 755
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3BDC 1.63 38.13 17464 17246 873 98.75 0.1815 0.1801 0.1813 0.208 0.2074 RANDOM 23.8861
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] -0.98 0.65 -1.14 2.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.305 r_dihedral_angle_3_deg 15.036 r_dihedral_angle_4_deg 9.98 r_dihedral_angle_1_deg 6.31 r_scangle_it 4.685 r_scbond_it 3.205 r_mcangle_it 2.133 r_angle_refined_deg 1.483 r_mcbond_it 1.39 r_chiral_restr 0.122
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.305 r_dihedral_angle_3_deg 15.036 r_dihedral_angle_4_deg 9.98 r_dihedral_angle_1_deg 6.31 r_scangle_it 4.685 r_scbond_it 3.205 r_mcangle_it 2.133 r_angle_refined_deg 1.483 r_mcbond_it 1.39 r_chiral_restr 0.122 r_gen_planes_refined 0.015 r_bond_refined_d 0.013
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1031 Nucleic Acid Atoms Solvent Atoms 81 Heterogen Atoms 26
Software Software Software Name Purpose SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction CBASS data collection HKL-2000 data reduction