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Crystal structure of Sulfolobus solfataricus Diphosphomevalonate decarboxylase in complex with ADP
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 3.11 60.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 151.289 α = 90 b = 151.289 β = 90 c = 104.422 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 2013-04-18 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 1.7 27.8 99.8 23 15.2 50337
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 1.7 27.75 47643 2551 99.8 0.1706 0.16893 0.1803 0.20204 0.2137 RANDOM 28.579
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
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.425 r_dihedral_angle_4_deg 19.172 r_dihedral_angle_3_deg 15.91 r_long_range_B_refined 8.63 r_long_range_B_other 8.595 r_dihedral_angle_1_deg 7.169 r_scangle_other 6.621 r_scbond_it 4.422 r_scbond_other 4.417 r_mcangle_other 3.825
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.425 r_dihedral_angle_4_deg 19.172 r_dihedral_angle_3_deg 15.91 r_long_range_B_refined 8.63 r_long_range_B_other 8.595 r_dihedral_angle_1_deg 7.169 r_scangle_other 6.621 r_scbond_it 4.422 r_scbond_other 4.417 r_mcangle_other 3.825 r_mcangle_it 3.821 r_mcbond_it 2.953 r_mcbond_other 2.933 r_angle_refined_deg 2.593 r_angle_other_deg 1.256 r_chiral_restr 0.185 r_bond_refined_d 0.026 r_gen_planes_refined 0.013 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 2597 Nucleic Acid Atoms Solvent Atoms 257 Heterogen Atoms 78
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing