☰ Navigation Tabs
Crystal structure of Staphylococcus aureus nucleoside diphosphate kinase complexed with CDP
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 6.8 298 0.1M Bis-Tris (pH 6.8) and 25% PEG mme 2000, Microbatch Crystallization, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.34 47.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 186.613 α = 90 b = 73.055 β = 108.23 c = 102.272 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 2010-05-10 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 2.9 97.14 99.9 0.076 6.9 4.1 29289 1 60.5
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 2.9 3.06 100 0.183 6.4 4 4274
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 2.9 34.19 27487 1473 98.8 0.25422 0.2521 0.2506 0.29288 0.2894 RANDOM 35.194
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 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.277 r_dihedral_angle_3_deg 18.067 r_dihedral_angle_4_deg 16.66 r_dihedral_angle_1_deg 6.253 r_scangle_it 2.92 r_scbond_it 1.614 r_angle_refined_deg 1.357 r_mcangle_it 1.013 r_mcbond_it 0.504 r_chiral_restr 0.097
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.277 r_dihedral_angle_3_deg 18.067 r_dihedral_angle_4_deg 16.66 r_dihedral_angle_1_deg 6.253 r_scangle_it 2.92 r_scbond_it 1.614 r_angle_refined_deg 1.357 r_mcangle_it 1.013 r_mcbond_it 0.504 r_chiral_restr 0.097 r_bond_refined_d 0.012 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9167 Nucleic Acid Atoms Solvent Atoms 72 Heterogen Atoms 52
Software Software Software Name Purpose MAR345dtb data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling