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Crystal structure of Staphylococcal nuclease variant Delta+PHS T62R at cryogenic temperature
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 277 24% MPD, 25 mM Potassium Phosphate, Calcium Chloride, 5% Glycerol, pdTp, pH 8.0, vapor diffusion, hanging drop, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.64 53.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.598 α = 90 b = 74.42 β = 90.22 c = 67.975 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 2008-10-28 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) R Sym 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 1.8 68.04 99.3 0.056 0.046 22.9 9.4 62888 62385 34.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.8 1.86 99.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.8 50 62385 62385 3162 99.64 0.207 0.207 0.205 0.2044 0.244 0.2389 RANDOM 26.557
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] 1.36 -0.42 -0.48 -0.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.287 r_dihedral_angle_4_deg 16.02 r_dihedral_angle_3_deg 15.359 r_scangle_it 6.585 r_dihedral_angle_1_deg 5.807 r_scbond_it 4.594 r_mcangle_it 2.763 r_mcbond_it 1.787 r_angle_refined_deg 1.239 r_chiral_restr 0.112
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.287 r_dihedral_angle_4_deg 16.02 r_dihedral_angle_3_deg 15.359 r_scangle_it 6.585 r_dihedral_angle_1_deg 5.807 r_scbond_it 4.594 r_mcangle_it 2.763 r_mcbond_it 1.787 r_angle_refined_deg 1.239 r_chiral_restr 0.112 r_gen_planes_refined 0.016 r_bond_refined_d 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4320 Nucleic Acid Atoms Solvent Atoms 478 Heterogen Atoms 128
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 scaling