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Crystal structure of Staphylococcus aureus nucleoside diphosphate kinase complexed with ADP and Vanadate
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 8.5 298 0.1M Tris-Cl (pH 8.5), 20% PEG 3350, Microbatch Crystallization, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.3 46.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 119.91 α = 90 b = 71.367 β = 108.04 c = 160.08 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 CCD MARMOSAIC 225 mm CCD Grazing angle 2.8 mrad 2010-10-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 1.73550 ESRF BM14
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 2.7 60.49 100 0.15 5.6 4.1 35635 1 67.6
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 2.7 2.85 100 0.462 2.1 4.1 5175
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 2.7 51.67 33709 1777 99.61 0.25181 0.25077 0.2563 0.27077 0.2841 RANDOM 64.821
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 0.03 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.319 r_dihedral_angle_4_deg 22.13 r_dihedral_angle_3_deg 17.531 r_dihedral_angle_1_deg 6.073 r_scangle_it 2.846 r_scbond_it 1.612 r_angle_refined_deg 1.417 r_mcangle_it 1.089 r_mcbond_it 0.551 r_chiral_restr 0.094
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.319 r_dihedral_angle_4_deg 22.13 r_dihedral_angle_3_deg 17.531 r_dihedral_angle_1_deg 6.073 r_scangle_it 2.846 r_scbond_it 1.612 r_angle_refined_deg 1.417 r_mcangle_it 1.089 r_mcbond_it 0.551 r_chiral_restr 0.094 r_bond_refined_d 0.012 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9232 Nucleic Acid Atoms Solvent Atoms 122 Heterogen Atoms 206
Software Software Software Name Purpose PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling