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Crystal structure of Staphylococcal nuclease variant Delta+PHS L36E 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 20% MPD, 25 mM potassium phosphate, calcium chloride, pdTp, pH 9, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.23 44.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 31.226 α = 90 b = 60.621 β = 92.96 c = 38.186 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 PIXEL DECTRIS PILATUS 6M Meridionally-bent fused silica mirror with palladium and uncoated stripes vertically-focusing at 6.6:1 demagnification 2011-04-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 1.10 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 1.5 50 98.1 0.046 16.3 7.8 22377 22377
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 1.53 84 0.155 2.9 964
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 (All) 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 1.6 38.14 18817 18817 966 99.94 0.1851 0.1851 0.1836 0.2118 0.2317 RANDOM 29.5614
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] 0.03 -0.04 0.07 -0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.457 r_dihedral_angle_3_deg 14.658 r_dihedral_angle_4_deg 11.094 r_dihedral_angle_1_deg 6.519 r_scangle_it 5.507 r_scbond_it 3.753 r_mcangle_it 2.315 r_angle_refined_deg 1.86 r_mcbond_it 1.507 r_chiral_restr 0.155
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.457 r_dihedral_angle_3_deg 14.658 r_dihedral_angle_4_deg 11.094 r_dihedral_angle_1_deg 6.519 r_scangle_it 5.507 r_scbond_it 3.753 r_mcangle_it 2.315 r_angle_refined_deg 1.86 r_mcbond_it 1.507 r_chiral_restr 0.155 r_bond_refined_d 0.018 r_gen_planes_refined 0.016
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1034 Nucleic Acid Atoms Solvent Atoms 91 Heterogen Atoms 26
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction CBASS data collection HKL-2000 data reduction HKL-2000 data scaling