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Cryogenic structure of Staphylococcal nuclease variant D+PHS/V23K
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 24% MPD, 25 mM potassium phosphate, pdTp (2 eq.), calcium chloride (3 eq.), pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.21 44.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 31.138 α = 90 b = 60.351 β = 93.86 c = 38.156 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 MERIDIONALLY-BENT FUSED SILICA MIRROR WITH PALLADIUM AND UNCOATED STRIPES VERTICALLY- FOCUSING AT 6.6:1 DEMAGNIFICATION 2009-02-19 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 1.6 23.65 97.5 0.054 22.4 3.7 18219 18219 27
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.6 1.66 97 0.252 6.3 3.9 2069
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 ENTRY 3BDC 1.6 23.65 18219 18219 937 97.65 0.18888 0.18888 0.18671 0.1861 0.22762 0.2287 RANDOM 23.602
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] -0.12 0.03 0.04 0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.339 r_dihedral_angle_3_deg 14.477 r_dihedral_angle_4_deg 7.137 r_dihedral_angle_1_deg 6.46 r_scangle_it 5.119 r_scbond_it 3.448 r_mcangle_it 2.33 r_angle_refined_deg 1.819 r_mcbond_it 1.479 r_chiral_restr 0.149
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.339 r_dihedral_angle_3_deg 14.477 r_dihedral_angle_4_deg 7.137 r_dihedral_angle_1_deg 6.46 r_scangle_it 5.119 r_scbond_it 3.448 r_mcangle_it 2.33 r_angle_refined_deg 1.819 r_mcbond_it 1.479 r_chiral_restr 0.149 r_bond_refined_d 0.019 r_gen_planes_refined 0.014
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1035 Nucleic Acid Atoms Solvent Atoms 111 Heterogen Atoms 26
Software Software Software Name Purpose CBASS data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling