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Crystal structure of Sulfolobus shibatae isopentenyl diphosphate isomerase in complex with FMN and DMAPP.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8 293 30% PEG 400, 0.2M sodium citrate, 0.1M Tris-HCl, pH 8.0, VAPOR DIFFUSION, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.63 53.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.071 α = 90 b = 101.071 β = 90 c = 333.43 γ = 90
Symmetry Space Group P 43 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 95 CCD ADSC QUANTUM 270 mirror 2008-03-05 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 1.0000, 1.13980, 1.14022, 1.04000 Photon Factory BL-17A
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 3 50 95.9 0.092 13.2 4.5 34495 64.4
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 3 3.11 90.9 0.092 2.1 3.7
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT 3 45.22 32758 1713 96.06 0.18564 0.18407 0.21473 0.182 RANDOM 47.268
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 37.559 r_dihedral_angle_4_deg 21.791 r_dihedral_angle_3_deg 19.659 r_dihedral_angle_1_deg 5.758 r_scangle_it 2.255 r_angle_refined_deg 1.472 r_scbond_it 1.288 r_mcangle_it 1.024 r_mcbond_it 0.568 r_symmetry_vdw_refined 0.331
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.559 r_dihedral_angle_4_deg 21.791 r_dihedral_angle_3_deg 19.659 r_dihedral_angle_1_deg 5.758 r_scangle_it 2.255 r_angle_refined_deg 1.472 r_scbond_it 1.288 r_mcangle_it 1.024 r_mcbond_it 0.568 r_symmetry_vdw_refined 0.331 r_nbtor_refined 0.314 r_symmetry_hbond_refined 0.268 r_nbd_refined 0.213 r_xyhbond_nbd_refined 0.148 r_chiral_restr 0.116 r_metal_ion_refined 0.02 r_bond_refined_d 0.012 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11232 Nucleic Acid Atoms Solvent Atoms 175 Heterogen Atoms 184
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling SHARP phasing