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Crystal structure of Sulfolobus shibatae isopentenyl diphosphate isomerase, octameric form
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8 293 0.1M Tris-HCl, 0.2M sodium citrate, 30% PEG 400, pH 8.0, VAPOR DIFFUSION, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.64 53.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.841 α = 90 b = 100.841 β = 90 c = 336.651 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) 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 1.7 50 94.7 8.5 180131
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.73 77.1
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 1.7 35.15 170951 9047 94.62 0.18644 0.185 0.1836 0.217 0.2147 RANDOM 23.746
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 35.912 r_dihedral_angle_4_deg 20.046 r_dihedral_angle_3_deg 16.277 r_dihedral_angle_1_deg 6.077 r_scangle_it 6.033 r_scbond_it 3.649 r_angle_refined_deg 2.628 r_mcangle_it 2.331 r_mcbond_it 1.319 r_chiral_restr 0.251
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.912 r_dihedral_angle_4_deg 20.046 r_dihedral_angle_3_deg 16.277 r_dihedral_angle_1_deg 6.077 r_scangle_it 6.033 r_scbond_it 3.649 r_angle_refined_deg 2.628 r_mcangle_it 2.331 r_mcbond_it 1.319 r_chiral_restr 0.251 r_bond_refined_d 0.033 r_gen_planes_refined 0.014 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 11200 Nucleic Acid Atoms Solvent Atoms 724 Heterogen Atoms 124
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling