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Crystal Structure of 2C-Methyl-D-Erythritol-2,4-cyclodiphosphate Synthase from Shewanella Oneidensis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GX1 PDB entry 1GX1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.8 295 formate, glycerol, TRIS, sodium chloride, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 3.6 65.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.088 α = 90 b = 117.088 β = 90 c = 108.937 γ = 90
Symmetry Space Group P 43 21 2
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 BRUKER SMART 6000 Montel mirrors 2003-07-17 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD BRANDEIS - B4 beam focused by a toroidal mirror 2003-07-29 M MAD 1,2 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE ENRAF-NONIUS FR591 1.5418 2 SYNCHROTRON NSLS BEAMLINE X12C .97911 NSLS X12C
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 1.6 81.65 0.081 0.081 55.7 14.5 99854 2 2
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) 1,2 1.6 1.66 100 0.5 0.5 5.9 13.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1GX1 1.6 29.8 99854 94783 4986 99.97 0.17526 0.17434 0.1886 0.19307 0.2088 RANDOM 15.215
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] -0.17 -0.17 0.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.808 r_scangle_it 4.55 r_scbond_it 2.87 r_mcangle_it 1.774 r_angle_refined_deg 1.603 r_mcbond_it 1.005 r_angle_other_deg 0.884 r_symmetry_hbond_refined 0.334 r_nbd_other 0.254 r_nbd_refined 0.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.808 r_scangle_it 4.55 r_scbond_it 2.87 r_mcangle_it 1.774 r_angle_refined_deg 1.603 r_mcbond_it 1.005 r_angle_other_deg 0.884 r_symmetry_hbond_refined 0.334 r_nbd_other 0.254 r_nbd_refined 0.23 r_xyhbond_nbd_refined 0.208 r_symmetry_vdw_other 0.205 r_metal_ion_refined 0.121 r_chiral_restr 0.111 r_symmetry_vdw_refined 0.086 r_nbtor_other 0.083 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_gen_planes_other 0.003 r_bond_other_d 0.002 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_other r_symmetry_hbond_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 3555 Nucleic Acid Atoms Solvent Atoms 583 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing