☰ Navigation Tabs
Crystal structure of Staphylococcus aureus nucleoside diphosphate kinase complexed with ADP
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 6.5 298 0.1M Bis-Tris, 6.5, 25% PEG 2000, Microbatch Crystallization, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.11 41.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.27 α = 90 b = 103.065 β = 90 c = 127 γ = 90
Symmetry Space Group P 21 21 21
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 2010-05-19 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 2.21 34.52 97.4 0.05 16.1 3.4 44437 1 22.4
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 2.21 2.33 89.2 0.208 5.6 3.2 5870
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 2.22 34.52 42078 2230 97.82 0.18389 0.18008 0.1804 0.25846 0.2559 RANDOM 18.436
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 35.428 r_dihedral_angle_4_deg 21.805 r_dihedral_angle_3_deg 16.884 r_dihedral_angle_1_deg 6.926 r_scangle_it 4.296 r_scbond_it 2.806 r_angle_refined_deg 2 r_mcangle_it 1.587 r_mcbond_it 0.853 r_chiral_restr 0.137
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.428 r_dihedral_angle_4_deg 21.805 r_dihedral_angle_3_deg 16.884 r_dihedral_angle_1_deg 6.926 r_scangle_it 4.296 r_scbond_it 2.806 r_angle_refined_deg 2 r_mcangle_it 1.587 r_mcbond_it 0.853 r_chiral_restr 0.137 r_bond_refined_d 0.021 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6958 Nucleic Acid Atoms Solvent Atoms 441 Heterogen Atoms 167
Software Software Software Name Purpose MAR345dtb data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling