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Crystal structure of mevalonate diphosphate decarboxylase from Staphylococcus aureus (monoclinic form)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 298 0.1M Tris, 1.8M sodium malonate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.1 60
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.495 α = 90 b = 53.061 β = 94.82 c = 100.882 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 4 mirrors 2004-11-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-3 0.931 ESRF ID14-3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.3 46.92 100 0.102 0.102 6.6 5.2 40530 40530 2 2 22
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.3 2.42 100 0.295 0.295 2.5 5.1 5875
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 SAD THROUGHOUT 2.3 46.92 40530 40530 2030 99.99 0.194 0.191 0.191 0.1905 0.249 0.247 RANDOM 14.837
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] 0.66 -0.24 -0.82 0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.874 r_dihedral_angle_4_deg 26.915 r_dihedral_angle_3_deg 19.824 r_dihedral_angle_1_deg 6.697 r_scangle_it 3.85 r_scbond_it 2.423 r_angle_refined_deg 1.805 r_mcangle_it 1.516 r_mcbond_it 0.915 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.874 r_dihedral_angle_4_deg 26.915 r_dihedral_angle_3_deg 19.824 r_dihedral_angle_1_deg 6.697 r_scangle_it 3.85 r_scbond_it 2.423 r_angle_refined_deg 1.805 r_mcangle_it 1.516 r_mcbond_it 0.915 r_nbtor_refined 0.301 r_symmetry_hbond_refined 0.257 r_symmetry_vdw_refined 0.222 r_nbd_refined 0.219 r_xyhbond_nbd_refined 0.187 r_chiral_restr 0.133 r_bond_refined_d 0.018 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5255 Nucleic Acid Atoms Solvent Atoms 406 Heterogen Atoms
Software Software Software Name Purpose SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction