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Crystal Structure of adenosine phosphate-isopentenyltransferase complexed with substrate analog, DMASPP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.8 277 1.4-2.0M sodium formate, 5mM magnesium chloride, 0.1M sodium acetate buffer, 20mM dimethylallyl S-thiolodiphosphate, pH 4.8-5.4., VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.62 53.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.417 α = 90 b = 96.417 β = 90 c = 65.068 γ = 90
Symmetry Space Group P 42 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 CCD RIGAKU JUPITER 210 2004-11-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL45PX 1.0000 SPring-8 BL45PX
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 68.2 98.29 17222 24.01
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 FOURIER SYNTHESIS THROUGHOUT 2.1 68.2 17222 934 98.29 0.19957 0.19633 0.2432 0.26424 0.2405 RANDOM 52.277
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] 3.08 3.08 -6.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.323 r_dihedral_angle_4_deg 21.642 r_dihedral_angle_3_deg 19.523 r_dihedral_angle_1_deg 7.028 r_scangle_it 5.124 r_scbond_it 3.615 r_angle_refined_deg 2.605 r_mcangle_it 2.112 r_mcbond_it 1.373 r_nbtor_refined 0.317
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.323 r_dihedral_angle_4_deg 21.642 r_dihedral_angle_3_deg 19.523 r_dihedral_angle_1_deg 7.028 r_scangle_it 5.124 r_scbond_it 3.615 r_angle_refined_deg 2.605 r_mcangle_it 2.112 r_mcbond_it 1.373 r_nbtor_refined 0.317 r_symmetry_hbond_refined 0.274 r_nbd_refined 0.239 r_xyhbond_nbd_refined 0.159 r_symmetry_vdw_refined 0.155 r_chiral_restr 0.153 r_bond_refined_d 0.026 r_gen_planes_refined 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1824 Nucleic Acid Atoms Solvent Atoms 38 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling