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Crystal structure of Staphylococcus aureus nucleoside diphosphate kinase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JXV PDB entry 1JXV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 Micobatch Crystallization 4.6 298 0.1M MgCl2, 0.1M Na-Acetate, pH 4.6, 20% PEG 2000, Micobatch Crystallization, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.02 39.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.615 α = 90 b = 91.615 β = 90 c = 176.876 γ = 120
Symmetry Space Group P 32 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 2009-11-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.9537 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 2.5 72.36 99.8 0.156 7.5 5.5 30434 1 30.8
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 2.64 100 0.38 3.8 5.5 4378
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 PDB entry 1JXV 2.5 45.81 28887 1533 99.72 0.21537 0.21252 0.2118 0.26863 0.2674 RANDOM 16.18
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.902 r_dihedral_angle_4_deg 20.896 r_dihedral_angle_3_deg 16.7 r_dihedral_angle_1_deg 6.301 r_scangle_it 2.923 r_scbond_it 1.757 r_angle_refined_deg 1.539 r_mcangle_it 1.116 r_mcbond_it 0.565 r_chiral_restr 0.121
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.902 r_dihedral_angle_4_deg 20.896 r_dihedral_angle_3_deg 16.7 r_dihedral_angle_1_deg 6.301 r_scangle_it 2.923 r_scbond_it 1.757 r_angle_refined_deg 1.539 r_mcangle_it 1.116 r_mcbond_it 0.565 r_chiral_restr 0.121 r_bond_refined_d 0.014 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6936 Nucleic Acid Atoms Solvent Atoms 429 Heterogen Atoms
Software Software Software Name Purpose PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling