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Crystal structure of Staphylococcal nuclease variant Delta+PHS M98G apo protein 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 7 277 34% MPD, 25 mM potassium phosphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.31 46.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.372 α = 90 b = 48.372 β = 90 c = 63.453 γ = 90
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 Meridianally-bent fused silica mirror with palladium and uncoated stripes vertically-focusing at 6.6:1 demagnification 2010-07-29 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 1.9 50 99.7 0.073 13.3 13.5 11646 11646 34.3
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 99.3 0.283 13.1 581
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 1.9 48.37 11629 11629 555 99.7 0.1669 0.1669 0.1648 0.1657 0.21 0.2126 RANDOM 12.6141
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] 0.59 0.59 -1.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.06 r_dihedral_angle_3_deg 15.921 r_dihedral_angle_4_deg 7.22 r_dihedral_angle_1_deg 6.103 r_scangle_it 5.445 r_scbond_it 3.606 r_mcangle_it 2.06 r_angle_refined_deg 1.704 r_mcbond_it 1.382 r_chiral_restr 0.159
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.06 r_dihedral_angle_3_deg 15.921 r_dihedral_angle_4_deg 7.22 r_dihedral_angle_1_deg 6.103 r_scangle_it 5.445 r_scbond_it 3.606 r_mcangle_it 2.06 r_angle_refined_deg 1.704 r_mcbond_it 1.382 r_chiral_restr 0.159 r_bond_refined_d 0.02 r_gen_planes_refined 0.013
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1029 Nucleic Acid Atoms Solvent Atoms 96 Heterogen Atoms 18
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 reduction HKL-2000 data scaling