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Crystal structure of PurN from Mycobacterium tuberculosis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MEO PDB entry 1MEO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 291 20% PEG 3350, 0.1 M Mg formate, 0.1 M NaI, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.32 46.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.273 α = 90 b = 73.366 β = 90 c = 77.246 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 MARMOSAIC 325 mm CCD 2007-07-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.97900 SSRL BL9-2
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 1.25 52.225 100 0.066 24.2 14.4 115083
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) 1.25 1.32 100 0.822 3.6 14.1
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1MEO 1.3 36.69 112329 102250 5129 99.53 0.16487 0.16374 0.18602 0.247 RANDOM 12.078
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] 0.16 -0.1 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.496 r_dihedral_angle_4_deg 14.491 r_dihedral_angle_3_deg 10.863 r_dihedral_angle_1_deg 5.584 r_sphericity_free 4.353 r_sphericity_bonded 4.135 r_scangle_it 3.625 r_scbond_it 2.409 r_mcangle_it 1.843 r_angle_refined_deg 1.335
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.496 r_dihedral_angle_4_deg 14.491 r_dihedral_angle_3_deg 10.863 r_dihedral_angle_1_deg 5.584 r_sphericity_free 4.353 r_sphericity_bonded 4.135 r_scangle_it 3.625 r_scbond_it 2.409 r_mcangle_it 1.843 r_angle_refined_deg 1.335 r_rigid_bond_restr 1.17 r_mcbond_it 1.115 r_chiral_restr 0.076 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 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_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3045 Nucleic Acid Atoms Solvent Atoms 449 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement Blu-Ice data collection MOSFLM data reduction SCALA data scaling PHASER phasing PHENIX refinement