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Diphosphomevalonate decarboxylase from the Sulfolobus solfataricus, space group h32
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HKE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 0.1M HEPES, 0.8M sodium phosphate monobasic, 0.8M potassium phosphate monobasic, 15% glycerol
Crystal Properties Matthews coefficient Solvent content 3.27 62.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 152.13 α = 90 b = 152.13 β = 90 c = 108.582 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 2013-01-26 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 2.2 45.3 96.4 22.6 15.4 23567
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 MOLECULAR REPLACEMENT THROUGHOUT 2HKE 2.2 45.26 21282 1116 91.1 0.21243 0.21112 0.2128 0.23709 0.2389 RANDOM 38.834
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] -0.9 -0.45 -0.9 2.92
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.9 r_dihedral_angle_4_deg 18.743 r_dihedral_angle_3_deg 17.82 r_long_range_B_refined 6.208 r_dihedral_angle_1_deg 5.824 r_mcangle_it 2.611 r_scbond_it 1.992 r_mcbond_it 1.521 r_angle_refined_deg 1.374 r_chiral_restr 0.087
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.9 r_dihedral_angle_4_deg 18.743 r_dihedral_angle_3_deg 17.82 r_long_range_B_refined 6.208 r_dihedral_angle_1_deg 5.824 r_mcangle_it 2.611 r_scbond_it 1.992 r_mcbond_it 1.521 r_angle_refined_deg 1.374 r_chiral_restr 0.087 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other 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 140 Heterogen Atoms 17
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling BALBES phasing