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Crystal structure of geranylgeranyl pyrophosphate synthase Rv0562 from Mycobacterium tuberculosis in complex with IPP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1WV0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9 298 30% PEG 6000, 0.6 M Bicine, pH 9.0
Crystal Properties Matthews coefficient Solvent content 2.36 47.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.796 α = 90 b = 115.643 β = 90 c = 119.27 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 PIXEL Bruker PHOTON III 2021-08-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 LIQUID ANODE BRUKER METALJET 1.34138
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 1.89 35.96 99.1 0.0402 30.7 7.04 54521
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 1.89 1.92 95.2 0.1302 6.75 3.66
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.89 32.78 51618 2697 98.9 0.14419 0.14156 0.1552 0.193 0.2037 RANDOM 16.037
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] -0.02 -0.57 0.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.39 r_dihedral_angle_4_deg 17.84 r_dihedral_angle_3_deg 12.587 r_long_range_B_refined 5.754 r_long_range_B_other 5.754 r_dihedral_angle_1_deg 5.333 r_scangle_other 3.967 r_scbond_it 2.553 r_scbond_other 2.553 r_mcangle_it 2.064
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.39 r_dihedral_angle_4_deg 17.84 r_dihedral_angle_3_deg 12.587 r_long_range_B_refined 5.754 r_long_range_B_other 5.754 r_dihedral_angle_1_deg 5.333 r_scangle_other 3.967 r_scbond_it 2.553 r_scbond_other 2.553 r_mcangle_it 2.064 r_mcangle_other 2.064 r_angle_refined_deg 1.647 r_angle_other_deg 1.492 r_mcbond_it 1.41 r_mcbond_other 1.41 r_chiral_restr 0.088 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4926 Nucleic Acid Atoms Solvent Atoms 919 Heterogen Atoms 113
Software Software Software Name Purpose REFMAC refinement SAINT data scaling SAINT data reduction PHASER phasing