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Crystal structure of Staphylococcal nuclease variant Delta+PHS V23K/I92A at cryogenic temperature
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BDC PDB ID: 3BDC Residues 7-141, deleted waters and cofactors, all B factors set to 20.00 A2, truncated: H8A, T13A, V23A, Q30A, K64A, T82A, I92A, Y113A, V114A, Y115A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 9 277 27% MPD, 25 mM Potassium Phosphate, Calcium Chloride, pdTp, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.21 44.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 31.131 α = 90 b = 60.448 β = 93.56 c = 37.972 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 mirrors 2009-07-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 0.97950 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 1.79 50 98 0.075 14.7 11.8 13067 13067 31.26
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 1.79 1.82 97 0.28 12.4 649
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ID: 3BDC Residues 7-141, deleted waters and cofactors,
all B factors set to 20.00 A2, truncated: H8A, T13A, V23A, Q30A, K64A, T82A, I92A, Y113A, V114A, Y115A 1.79 22.94 13040 13040 1298 98.06 0.1841 0.1841 0.1791 0.1814 0.2307 0.2303 RANDOM 24.8326
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] -1.76 0.37 -1.31 3.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.724 r_dihedral_angle_4_deg 18.262 r_dihedral_angle_3_deg 16.062 r_dihedral_angle_1_deg 6.37 r_scangle_it 4.715 r_scbond_it 3.27 r_mcangle_it 1.946 r_angle_refined_deg 1.499 r_mcbond_it 1.252 r_chiral_restr 0.122
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.724 r_dihedral_angle_4_deg 18.262 r_dihedral_angle_3_deg 16.062 r_dihedral_angle_1_deg 6.37 r_scangle_it 4.715 r_scbond_it 3.27 r_mcangle_it 1.946 r_angle_refined_deg 1.499 r_mcbond_it 1.252 r_chiral_restr 0.122 r_bond_refined_d 0.014 r_gen_planes_refined 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1032 Nucleic Acid Atoms Solvent Atoms 61 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