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Crystal structure of glycine cleavage system protein H from Mycobacterium tuberculosis, using X-rays from the Compact Light Source.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3HGB pdb entry 3hgb
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.3 290 1.5M SODIUM CITRATE, 50MM BISTRIS PH 6.3; MYTUD.01046.A AT 27MG/ML, , VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.35 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.45 α = 90 b = 51.01 β = 95.1 c = 32.57 γ = 90
Symmetry Space Group C 1 2 1
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 MAR CCD 165 mm 2009-07-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON OTHER 0.81836
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 20 98.8 0.095 10.17 3.1 9535 9535 -3 21.39
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) 2 2.05 99.3 0.385 3.2 3.1 710
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT pdb entry 3hgb 2 20 9535 9535 459 98.9 0.185 0.181 0.1828 0.253 0.2507 RANDOM 12.01
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] -0.1 0.21 0.76 -0.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.103 r_dihedral_angle_4_deg 24.186 r_dihedral_angle_3_deg 11.988 r_dihedral_angle_1_deg 7.182 r_scangle_it 3.677 r_scbond_it 2.352 r_mcangle_it 1.668 r_angle_refined_deg 1.586 r_mcbond_it 0.919 r_angle_other_deg 0.858
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.103 r_dihedral_angle_4_deg 24.186 r_dihedral_angle_3_deg 11.988 r_dihedral_angle_1_deg 7.182 r_scangle_it 3.677 r_scbond_it 2.352 r_mcangle_it 1.668 r_angle_refined_deg 1.586 r_mcbond_it 0.919 r_angle_other_deg 0.858 r_mcbond_other 0.211 r_chiral_restr 0.076 r_bond_refined_d 0.016 r_gen_planes_refined 0.006 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 999 Nucleic Acid Atoms Solvent Atoms 161 Heterogen Atoms
Software Software Software Name Purpose MOLREP phasing REFMAC refinement XDS data reduction XSCALE data scaling