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Crystal structure of Sulfolobus shibatae isopentenyl diphosphate isomerase in complex with reduced 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 53.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.842 α = 90 b = 100.842 β = 90 c = 334.499 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 210r 2009-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.000 Photon Factory BL-5A
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 2.29 50 93.8 0.113 22.5 6 73441
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 2.3 2.34 98.8 0.355 5.7 6.5
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 MOLECULAR REPLACEMENT THROUGHOUT 2.29 37.39 69424 3699 93.46 0.20595 0.20416 0.1994 0.23883 0.233 RANDOM 46.232
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 36.305 r_dihedral_angle_4_deg 21.031 r_dihedral_angle_3_deg 17.855 r_dihedral_angle_1_deg 6.165 r_scangle_it 5.212 r_scbond_it 3.128 r_angle_refined_deg 1.975 r_mcangle_it 1.85 r_mcbond_it 0.962 r_chiral_restr 0.173
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.305 r_dihedral_angle_4_deg 21.031 r_dihedral_angle_3_deg 17.855 r_dihedral_angle_1_deg 6.165 r_scangle_it 5.212 r_scbond_it 3.128 r_angle_refined_deg 1.975 r_mcangle_it 1.85 r_mcbond_it 0.962 r_chiral_restr 0.173 r_bond_refined_d 0.023 r_gen_planes_refined 0.009 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11232 Nucleic Acid Atoms Solvent Atoms 294 Heterogen Atoms 184
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling