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Crystal structure of adenylate kinase from burkholderia pseudomallei
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 290 HAMPTON SCREEN, B5: 30% PEG 4000, 200MM LI2SO4, 100MM TRIS PH 8,, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.27 46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.23 α = 90 b = 66 β = 113.69 c = 63.76 γ = 90
Symmetry Space Group P 1 21 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 ADSC QUANTUM Q315r 2009-01-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X8C 0.9791 NSLS X8C
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 2.1 20 99.5 0.072 17.02 7.4 27839 27703 -3 42.51
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.15 99.8 0.618 0.618 3.1 7.6 2051
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 SAD THROUGHOUT 2.1 20 27715 26320 1395 99.8 0.238 0.238 0.235 0.2362 0.295 0.2948 RANDOM 29.82
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] -0.53 -0.19 1.7 -1.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.292 r_dihedral_angle_4_deg 19.387 r_dihedral_angle_3_deg 14.881 r_dihedral_angle_1_deg 6.19 r_scangle_it 4.024 r_scbond_it 2.578 r_angle_refined_deg 1.521 r_mcangle_it 1.478 r_angle_other_deg 0.874 r_mcbond_it 0.802
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.292 r_dihedral_angle_4_deg 19.387 r_dihedral_angle_3_deg 14.881 r_dihedral_angle_1_deg 6.19 r_scangle_it 4.024 r_scbond_it 2.578 r_angle_refined_deg 1.521 r_mcangle_it 1.478 r_angle_other_deg 0.874 r_mcbond_it 0.802 r_mcbond_other 0.173 r_chiral_restr 0.079 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3084 Nucleic Acid Atoms Solvent Atoms 216 Heterogen Atoms 20
Software Software Software Name Purpose SHARP phasing PARROT phasing ARP/wARP model building REFMAC refinement XDS data reduction XSCALE data scaling