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Crystal structure of Staphylococcus aureus nucleoside diphosphate kinase complexed with GTP
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 5 298 0.1M Mgacetate, 0.1M citric acid, pH 5, 14% PEG 8000 , Microbatch Crystallization, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.39 48.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.302 α = 90 b = 75.302 β = 90 c = 154.712 γ = 120
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 Goebel Mirrors 2010-05-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR 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 2.36 37.65 96.8 0.03 46.4 7.6 13104 1 29.3
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 2.36 2.48 78.5 0.081 20.4 7 1550
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 2.38 37.65 12456 644 99.54 0.16877 0.16626 0.1704 0.22011 0.2202 RANDOM 19.665
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] -0.01 -0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.888 r_dihedral_angle_4_deg 25.788 r_dihedral_angle_3_deg 16.842 r_dihedral_angle_1_deg 6.983 r_scangle_it 4.678 r_scbond_it 2.782 r_angle_refined_deg 1.926 r_mcangle_it 1.555 r_mcbond_it 0.794 r_chiral_restr 0.126
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.888 r_dihedral_angle_4_deg 25.788 r_dihedral_angle_3_deg 16.842 r_dihedral_angle_1_deg 6.983 r_scangle_it 4.678 r_scbond_it 2.782 r_angle_refined_deg 1.926 r_mcangle_it 1.555 r_mcbond_it 0.794 r_chiral_restr 0.126 r_bond_refined_d 0.02 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2290 Nucleic Acid Atoms Solvent Atoms 135 Heterogen Atoms 66
Software Software Software Name Purpose MAR345dtb data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling