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Crystal structure of phosphoribosylpyrophosphate synthetase from Mycobacterium smegmatis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DKR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 277.15 0.2M NaCl, 0.1M Sodium acetate, 30% (v/v) 2-Methyl-2,4-pentanediol
Crystal Properties Matthews coefficient Solvent content 2.33 47.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.292 α = 90 b = 85.292 β = 90 c = 249.791 γ = 90
Symmetry Space Group P 41 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 PIXEL DECTRIS PILATUS 6M 2013-09-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.98 ESRF ID23-1
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 2.4 43.38 96.18 0.067 6.24 1.9 35723 38.07
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 2.4 2.49 97.26 0.34 2.34 1.9
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 1DKR 2.4 50.01 33860 1820 96.19 0.1996 0.19817 0.2053 0.2255 0.23 RANDOM 42.983
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] -2.53 -2.53 5.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.107 r_dihedral_angle_4_deg 19.278 r_dihedral_angle_3_deg 16.216 r_long_range_B_refined 12.159 r_long_range_B_other 12.159 r_scangle_other 8.146 r_dihedral_angle_1_deg 6.186 r_scbond_it 5.047 r_scbond_other 5.047 r_mcangle_it 4.831
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.107 r_dihedral_angle_4_deg 19.278 r_dihedral_angle_3_deg 16.216 r_long_range_B_refined 12.159 r_long_range_B_other 12.159 r_scangle_other 8.146 r_dihedral_angle_1_deg 6.186 r_scbond_it 5.047 r_scbond_other 5.047 r_mcangle_it 4.831 r_mcangle_other 4.83 r_mcbond_it 3.133 r_mcbond_other 3.119 r_angle_refined_deg 1.65 r_angle_other_deg 1.549 r_chiral_restr 0.086 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 r_bond_other_d 0.007 r_gen_planes_other 0.006 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 6864 Nucleic Acid Atoms Solvent Atoms 68 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing