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Crystal structure of Sulfolobus solfataricus diphosphomevalonate decarboxylase in complex with ATP-gamma-S
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4Z7C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 4.6 293 0.1M sodium acetate, 1.5M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 3.1 60.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 151.238 α = 90 b = 151.238 β = 90 c = 104.416 γ = 120
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 2013-11-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.000 Photon Factory AR-NW12A
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 1.5 48.5 99.2 37.1 10 72082
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 FOURIER SYNTHESIS THROUGHOUT 4Z7C 1.5 48.5 68482 3638 99.09 0.16623 0.16486 0.1748 0.19234 0.1992 RANDOM 21.095
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 35.189 r_dihedral_angle_4_deg 16.759 r_dihedral_angle_3_deg 14.315 r_long_range_B_refined 9.708 r_long_range_B_other 9.667 r_dihedral_angle_1_deg 6.523 r_scangle_other 6.513 r_scbond_it 4.558 r_scbond_other 4.499 r_mcangle_other 3.268
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.189 r_dihedral_angle_4_deg 16.759 r_dihedral_angle_3_deg 14.315 r_long_range_B_refined 9.708 r_long_range_B_other 9.667 r_dihedral_angle_1_deg 6.523 r_scangle_other 6.513 r_scbond_it 4.558 r_scbond_other 4.499 r_mcangle_other 3.268 r_mcangle_it 3.265 r_angle_refined_deg 2.956 r_mcbond_it 2.407 r_mcbond_other 2.396 r_angle_other_deg 1.36 r_chiral_restr 0.23 r_bond_refined_d 0.031 r_gen_planes_refined 0.014 r_bond_other_d 0.003 r_gen_planes_other 0.002 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2605 Nucleic Acid Atoms Solvent Atoms 243 Heterogen Atoms 82
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing