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Crystal Structure of adenosine phosphate-isopentenyltransferase complexed with diphosphate
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 diphosphate, pH 4.8-5.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.7 54.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.51 α = 90 b = 97.568 β = 90 c = 131.108 γ = 90
Symmetry Space Group P 21 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 2004-01-01 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 2.8 131.31 97.83 29244 39.384
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 2.8 131.31 29244 1566 97.83 0.23385 0.2303 0.2313 0.30218 0.3011 RANDOM 85.639
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] 3.88 4.1 -7.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.186 r_dihedral_angle_4_deg 24.805 r_dihedral_angle_3_deg 24.088 r_dihedral_angle_1_deg 8.853 r_angle_refined_deg 2.975 r_mcangle_it 1.884 r_scangle_it 1.818 r_scbond_it 1.15 r_mcbond_it 1.148 r_nbtor_refined 0.377
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.186 r_dihedral_angle_4_deg 24.805 r_dihedral_angle_3_deg 24.088 r_dihedral_angle_1_deg 8.853 r_angle_refined_deg 2.975 r_mcangle_it 1.884 r_scangle_it 1.818 r_scbond_it 1.15 r_mcbond_it 1.148 r_nbtor_refined 0.377 r_symmetry_vdw_refined 0.375 r_symmetry_hbond_refined 0.368 r_nbd_refined 0.337 r_xyhbond_nbd_refined 0.272 r_chiral_restr 0.169 r_bond_refined_d 0.032 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7260 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling