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Crystal Structure of Manganese-metallated GTP Cyclohydrolase Type IB
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3D1T PDB entry 3D1T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 298 (PEG 6000, 10-16%), LiCl (1-1.4 M), Tris (50 mM, pH 9.0) and Tris-Cl (50 mM, pH 7.0).
Enzym sample prepared at 10 mg/mL in 50 mM Tris-HCl, 50 mM KCl, 1 mM DTT, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.29 46.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.225 α = 90 b = 100.42 β = 90 c = 113.947 γ = 90
Symmetry Space Group C 2 2 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 CCD ADSC QUANTUM 315 2008-03-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL7-1 0.97607 SSRL BL7-1
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 2.04 50 99.8 0.071 11 4.5 33675 33675
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 2.04 2.11 99.9 0.428 4.5 3314
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 3D1T 2.04 30.33 33647 1710 99.66 0.189 0.185 0.1927 0.264 RANDOM 37.382
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] -0.09 0.02 0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.185 r_dihedral_angle_4_deg 22.331 r_dihedral_angle_3_deg 16.604 r_sphericity_free 8.842 r_dihedral_angle_1_deg 6.962 r_scangle_it 4.451 r_sphericity_bonded 4.391 r_scbond_it 3.29 r_rigid_bond_restr 2.302 r_mcangle_it 2.184
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.185 r_dihedral_angle_4_deg 22.331 r_dihedral_angle_3_deg 16.604 r_sphericity_free 8.842 r_dihedral_angle_1_deg 6.962 r_scangle_it 4.451 r_sphericity_bonded 4.391 r_scbond_it 3.29 r_rigid_bond_restr 2.302 r_mcangle_it 2.184 r_angle_refined_deg 1.754 r_mcbond_it 1.42 r_nbtor_refined 0.302 r_symmetry_vdw_refined 0.24 r_nbd_refined 0.22 r_metal_ion_refined 0.181 r_symmetry_hbond_refined 0.167 r_xyhbond_nbd_refined 0.158 r_chiral_restr 0.122 r_bond_refined_d 0.019 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3829 Nucleic Acid Atoms Solvent Atoms 261 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling CNS refinement DENZO data reduction PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction CNS phasing