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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 53.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.879 α = 90 b = 100.879 β = 90 c = 334.864 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 2008-06-29 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 2.9 50 99.6 0.09 22.1 11.9 39430 63.6
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 2.9 3 96.9 0.412 2.5 6.1
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 2.9 48.85 37374 1970 99.49 0.19318 0.19212 0.1923 0.2129 0.2115 RANDOM 45.543
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] -0.01 -0.01 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.368 r_dihedral_angle_4_deg 23.408 r_dihedral_angle_3_deg 19.83 r_dihedral_angle_1_deg 5.53 r_scangle_it 2.561 r_angle_refined_deg 1.572 r_scbond_it 1.449 r_mcangle_it 1.265 r_mcbond_it 0.734 r_symmetry_vdw_refined 0.344
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.368 r_dihedral_angle_4_deg 23.408 r_dihedral_angle_3_deg 19.83 r_dihedral_angle_1_deg 5.53 r_scangle_it 2.561 r_angle_refined_deg 1.572 r_scbond_it 1.449 r_mcangle_it 1.265 r_mcbond_it 0.734 r_symmetry_vdw_refined 0.344 r_nbtor_refined 0.311 r_symmetry_hbond_refined 0.259 r_nbd_refined 0.212 r_chiral_restr 0.177 r_xyhbond_nbd_refined 0.151 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 172 Heterogen Atoms 184
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling SHARP phasing