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Crystal structure of Staphylococcus aureus nucleoside diphosphate kinase complexed with UDP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3Q83
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 Microbatch Crystallization 7.2 298 0.1M Bis-Tris, pH 7.2, 30% PEG 3350, Microbatch Crystallization , temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.33 47.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 186.665 α = 90 b = 72.916 β = 108.42 c = 102.144 γ = 90
Symmetry Space Group C 1 2 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 IMAGE PLATE MAR scanner 345 mm plate VariMax 2010-06-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 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 2.5 34.12 99.6 0.09 11.6 5.2 45083 1 41.5
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 2.5 2.64 99.1 0.333 4.8 5.2 6465
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 3Q83 2.5 32.3 42809 2268 99.51 0.23296 0.23031 0.233 0.28286 0.282 RANDOM 37.304
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] -0.02 -0.01 0.02 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.124 r_dihedral_angle_4_deg 18.66 r_dihedral_angle_3_deg 15.964 r_dihedral_angle_1_deg 6.338 r_scangle_it 3.064 r_scbond_it 1.8 r_angle_refined_deg 1.526 r_mcangle_it 1.109 r_mcbond_it 0.581 r_chiral_restr 0.107
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.124 r_dihedral_angle_4_deg 18.66 r_dihedral_angle_3_deg 15.964 r_dihedral_angle_1_deg 6.338 r_scangle_it 3.064 r_scbond_it 1.8 r_angle_refined_deg 1.526 r_mcangle_it 1.109 r_mcbond_it 0.581 r_chiral_restr 0.107 r_bond_refined_d 0.015 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9159 Nucleic Acid Atoms Solvent Atoms 211 Heterogen Atoms 78
Software Software Software Name Purpose MAR345dtb data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling