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Crystal structure of Staphylococcal nuclease variant Delta+PHS T62E/V66E 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 8 277 25% MPD, 25 mM potassium phosphate, calcium chloride, pdTp
Crystal Properties Matthews coefficient Solvent content 2.2 44.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 31.108 α = 90 b = 60.399 β = 94.41 c = 38.013 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 110 CCD APEX II CCD mirrors 2015-01-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE OTHER 1.54
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 50 100 0.0274 25.61 12.67 11137 11137 26.94
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 0.151 8.04
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 1.9 32.12 10534 526 99.42 0.1801 0.1776 0.1905 0.2268 0.2224 RANDOM 24.784
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] -0.95 0.62 -1.53 2.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.557 r_dihedral_angle_3_deg 17.178 r_dihedral_angle_4_deg 8.327 r_dihedral_angle_1_deg 7.049 r_angle_refined_deg 1.75 r_mcangle_it 1.687 r_mcbond_it 1.144 r_mcbond_other 1.092 r_angle_other_deg 0.819 r_chiral_restr 0.117
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.557 r_dihedral_angle_3_deg 17.178 r_dihedral_angle_4_deg 8.327 r_dihedral_angle_1_deg 7.049 r_angle_refined_deg 1.75 r_mcangle_it 1.687 r_mcbond_it 1.144 r_mcbond_other 1.092 r_angle_other_deg 0.819 r_chiral_restr 0.117 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 r_bond_other_d 0.004 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1037 Nucleic Acid Atoms Solvent Atoms 99 Heterogen Atoms 26
Software Software Software Name Purpose APEX data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction APEX data reduction Coot model building