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Structure of mevalonate pyrophosphate decarboxylase from Streptococcus pyogenes
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.5 291 0.1M sodium acetate trihydrate, 25% PEG 3350, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 1.97 37.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.994 α = 90 b = 72.065 β = 90 c = 99.991 γ = 90
Symmetry Space Group P 21 21 21
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 315 2005-02-06 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97908, 0.97919 APS 19-ID
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 33.9 99.7 43511 43511
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.56 99.9 8.1
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 (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 1.5 33.9 43511 43511 2316 99.7 0.16651 0.16509 0.1642 0.19363 0.1931 RANDOM 22.419
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] -0.25 0.48 -0.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.64 r_dihedral_angle_4_deg 17.28 r_dihedral_angle_3_deg 12.892 r_dihedral_angle_1_deg 5.883 r_scangle_it 4.184 r_scbond_it 2.822 r_angle_refined_deg 1.484 r_mcangle_it 1.477 r_mcbond_it 1.099 r_symmetry_vdw_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.64 r_dihedral_angle_4_deg 17.28 r_dihedral_angle_3_deg 12.892 r_dihedral_angle_1_deg 5.883 r_scangle_it 4.184 r_scbond_it 2.822 r_angle_refined_deg 1.484 r_mcangle_it 1.477 r_mcbond_it 1.099 r_symmetry_vdw_refined 0.309 r_nbtor_refined 0.306 r_symmetry_hbond_refined 0.257 r_nbd_refined 0.219 r_xyhbond_nbd_refined 0.168 r_chiral_restr 0.107 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2447 Nucleic Acid Atoms Solvent Atoms 494 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement SBC-Collect data collection HKL-2000 data scaling HKL-3000 phasing SHELX phasing CCP4 phasing MLPHARE phasing DM phasing SOLVE phasing RESOLVE phasing O model building ARP/wARP model building Coot model building