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Crystal structure of IspD from Mycobacterium smegmatis in complex with CTP and Mg
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VGT PDB ENTRY 1VGT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 SITTING-DROP VAPOR-DIFFUSION METHOD AT 293 K. DROPS WITH 300 NANOLITERS PROTEIN SOLUTION (PROTEIN AT 40 MG/ML IN 20 MM BIS-TRIS-PROPANE, PH 6.5, 0.1 M NACL WITH 10 MM CTP AND 10 MM MGCL2) AND 300 NANOLITERS SCREENING/RESERVOIR SOLUTION (10% (W/V) PEG 8000, 20% (V/V) ETHYLENE GLYCOL, 0.03 M EACH OF DIETHYLENEGLYCOL, TRIETHYLENEGLYCOL, TETRAETHYLENEGLYCOL, PENTAETHYLENEGLYCOL AND 0.1 M MES/IMIDAZOLE BUFFERS PH 6.5)
Crystal Properties Matthews coefficient Solvent content 2.17 43.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.33 α = 90 b = 72.98 β = 90 c = 117.18 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 110 CCD ADSC QUANTUM 315r 2010-02-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 ESRF ID14-4
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 1.49 38.5 99.6 0.06 18.6 7.6 64486
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 1.49 1.57 99.5 0.41 5.3 7.5
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1VGT 1.49 61.95 61154 3262 99.5 0.186 0.185 0.21 0.2205 RANDOM 23.05
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] 1.08 -0.84 -0.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.703 r_dihedral_angle_4_deg 14.62 r_dihedral_angle_3_deg 11.769 r_dihedral_angle_1_deg 5.173 r_angle_refined_deg 1.29 r_chiral_restr 0.073 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.703 r_dihedral_angle_4_deg 14.62 r_dihedral_angle_3_deg 11.769 r_dihedral_angle_1_deg 5.173 r_angle_refined_deg 1.29 r_chiral_restr 0.073 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 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_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it 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 3166 Nucleic Acid Atoms Solvent Atoms 470 Heterogen Atoms 60
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing