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Mycobacterium smegmatis 2C-methyl-D-erythritol-2,4-cyclodiphosphate synthase (IspF)
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 6.5 18% PEG 8000, 0.1 M SODIUM CACODYLATE PH 6.5, 0.2 M CALCIUM ACETATE
Crystal Properties Matthews coefficient Solvent content 3.15 60.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 159.121 α = 90 b = 159.121 β = 90 c = 54.16 γ = 90
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 MARRESEARCH PT COATED MIRRORS IN A KIRKPATRICK-BAEZ (KB) GEOMETRY 2006-05-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 ESRF ID23-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.2 51.3 95.4 0.08 6 3.5 33193
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 3.11 76.3 0.35 1.7 2.1
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 PDB ENTRY 1GX1 2.2 51.3 31702 1671 100 0.165 0.163 0.1636 0.206 0.2072 RANDOM 28.25
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] -0.14 -0.14 0.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.135 r_dihedral_angle_4_deg 22.03 r_dihedral_angle_3_deg 17.5 r_dihedral_angle_1_deg 6.267 r_scangle_it 3.923 r_mcangle_it 3.633 r_scbond_it 2.669 r_mcbond_it 2.488 r_angle_refined_deg 1.57 r_nbtor_refined 0.293
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.135 r_dihedral_angle_4_deg 22.03 r_dihedral_angle_3_deg 17.5 r_dihedral_angle_1_deg 6.267 r_scangle_it 3.923 r_mcangle_it 3.633 r_scbond_it 2.669 r_mcbond_it 2.488 r_angle_refined_deg 1.57 r_nbtor_refined 0.293 r_nbd_refined 0.214 r_symmetry_hbond_refined 0.211 r_symmetry_vdw_refined 0.181 r_xyhbond_nbd_refined 0.178 r_chiral_restr 0.101 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined 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 3275 Nucleic Acid Atoms Solvent Atoms 272 Heterogen Atoms 136
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling AMoRE phasing