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Crystal structure of Staphylcoccal nulease variant Delta+PHS V66E L125E at cryogenic temperature
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BDC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 277 20% MPD, 25mM potassium phosphate, calcium chloride, pdTp
Crystal Properties Matthews coefficient Solvent content 2.22 44.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 31.14 α = 90 b = 60.315 β = 94.05 c = 38.364 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 multi-layer optics 2014-08-04 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 1.65 38.27 99.9 0.01 142.68 27.81 17155 17155 24.6
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 1.65 1.67 97.6 0.1398 6.63 8.71
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 3BDC 1.65 38.27 16239 864 99.68 0.1842 0.1823 0.1932 0.22 0.2378 RANDOM 20.713
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] -1.02 0.53 -1.06 1.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.449 r_dihedral_angle_3_deg 12.889 r_dihedral_angle_4_deg 10.214 r_dihedral_angle_1_deg 6.587 r_mcangle_it 2.752 r_mcbond_it 1.987 r_mcbond_other 1.95 r_angle_refined_deg 1.62 r_angle_other_deg 0.741 r_chiral_restr 0.103
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.449 r_dihedral_angle_3_deg 12.889 r_dihedral_angle_4_deg 10.214 r_dihedral_angle_1_deg 6.587 r_mcangle_it 2.752 r_mcbond_it 1.987 r_mcbond_other 1.95 r_angle_refined_deg 1.62 r_angle_other_deg 0.741 r_chiral_restr 0.103 r_bond_refined_d 0.017 r_gen_planes_refined 0.011 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1036 Nucleic Acid Atoms Solvent Atoms 94 Heterogen Atoms 26
Software Software Software Name Purpose SAINT data scaling SAINT data reduction PHASER phasing REFMAC refinement PDB_EXTRACT data extraction