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Crystal structure of Sulfolobus shibatae isopentenyl diphosphate isomerase in complex with FMN
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 2.64 53.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.745 α = 90 b = 100.745 β = 90 c = 336.829 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 210 mirror 2008-02-20 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0000, 1.13980, 1.14022, 1.04000 Photon Factory AR-NW12A
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 1.99 50 99.4 0.087 24.6 8.4 119401 25
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 1.99 2.06 96.9 0.268 8.3 8.1
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 MAD THROUGHOUT 2 37.5 110468 5826 97.99 0.18747 0.1856 0.1862 0.22253 0.2232 RANDOM 29.544
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 35.612 r_dihedral_angle_4_deg 24.544 r_dihedral_angle_3_deg 17.17 r_dihedral_angle_1_deg 5.76 r_scangle_it 3.216 r_scbond_it 2.108 r_angle_refined_deg 1.462 r_mcangle_it 1.324 r_mcbond_it 0.854 r_nbtor_refined 0.311
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.612 r_dihedral_angle_4_deg 24.544 r_dihedral_angle_3_deg 17.17 r_dihedral_angle_1_deg 5.76 r_scangle_it 3.216 r_scbond_it 2.108 r_angle_refined_deg 1.462 r_mcangle_it 1.324 r_mcbond_it 0.854 r_nbtor_refined 0.311 r_symmetry_vdw_refined 0.217 r_nbd_refined 0.214 r_xyhbond_nbd_refined 0.169 r_symmetry_hbond_refined 0.149 r_chiral_restr 0.105 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 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 10996 Nucleic Acid Atoms Solvent Atoms 728 Heterogen Atoms 124
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling SHARP phasing