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Crystal structure of deoxyribonucleotidase-like protein (NP_764060.1) from Staphylococcus epidermidis ATCC 12228 at 1.55 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 NANODROP, 17.6% PEG 3350, 0.4M Magnesium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.87 34.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.31 α = 71.93 b = 40.27 β = 75.08 c = 55.31 γ = 83.62
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 MARMOSAIC 325 mm CCD Flat mirror (vertical focusing) 2007-12-09 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.91837, 0.97908, 0.97959 SSRL BL11-1
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 1.54 29.235 92.8 0.067 4.92 43195 -3 27.438
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 1.54 1.6 75.2 0.529 1.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT 1.55 29.235 43194 2176 94.9 0.184 0.182 0.223 0.256 RANDOM 19.268
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 -0.21 -0.58 -0.79 0.77 0.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.647 r_dihedral_angle_4_deg 21.593 r_dihedral_angle_3_deg 13.772 r_dihedral_angle_1_deg 5.971 r_scangle_it 4.812 r_scbond_it 3.105 r_mcangle_it 1.748 r_angle_refined_deg 1.634 r_angle_other_deg 1.044 r_mcbond_it 1.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.647 r_dihedral_angle_4_deg 21.593 r_dihedral_angle_3_deg 13.772 r_dihedral_angle_1_deg 5.971 r_scangle_it 4.812 r_scbond_it 3.105 r_mcangle_it 1.748 r_angle_refined_deg 1.634 r_angle_other_deg 1.044 r_mcbond_it 1.004 r_mcbond_other 0.301 r_chiral_restr 0.104 r_bond_refined_d 0.017 r_gen_planes_refined 0.007 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2700 Nucleic Acid Atoms Solvent Atoms 181 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SOLVE phasing MolProbity model building XSCALE data scaling PDB_EXTRACT data extraction MAR345 data collection XDS data reduction