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Crystal structure of Histidinol-phosphate aminotransferase (EC 2.6.1.9) (Imidazole acetol-phosphate transferase) (tm1040) from Thermotoga maritima at 2.40 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UU0 pdb entry 1uu0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP, NANODROP 6.5 293 0.2M MgCl2, 20.0% PEG-1000, 0.1M Cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.4 48.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 145.156 α = 90 b = 187.453 β = 90 c = 54.316 γ = 90
Symmetry Space Group P 21 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 CCD ADSC QUANTUM 315 double crystal monochromator 2005-02-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 1.000001 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 2.4 29.8 91.7 0.079 9.3 2.7 54470
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 2.44 90.1 0.562 1.8 2.6
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 (All) 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 1uu0 2.4 29.6 51626 2745 91.54 0.185 0.18469 0.182 0.238 0.3022 RANDOM 53.956
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] 2.09 -1.39 -0.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.403 r_dihedral_angle_4_deg 19.709 r_dihedral_angle_3_deg 14.307 r_dihedral_angle_1_deg 5.902 r_scangle_it 5.549 r_scbond_it 3.733 r_mcangle_it 1.896 r_angle_refined_deg 1.228 r_mcbond_it 1.178 r_angle_other_deg 0.798
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.403 r_dihedral_angle_4_deg 19.709 r_dihedral_angle_3_deg 14.307 r_dihedral_angle_1_deg 5.902 r_scangle_it 5.549 r_scbond_it 3.733 r_mcangle_it 1.896 r_angle_refined_deg 1.228 r_mcbond_it 1.178 r_angle_other_deg 0.798 r_mcbond_other 0.302 r_symmetry_vdw_other 0.257 r_nbd_refined 0.19 r_nbtor_refined 0.18 r_nbd_other 0.177 r_symmetry_hbond_refined 0.154 r_xyhbond_nbd_refined 0.152 r_symmetry_vdw_refined 0.14 r_nbtor_other 0.083 r_chiral_restr 0.068 r_xyhbond_nbd_other 0.056 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10520 Nucleic Acid Atoms Solvent Atoms 339 Heterogen Atoms 116
Software Software Software Name Purpose REFMAC refinement SCALA data scaling PDB_EXTRACT data extraction DENZO data reduction SCALEPACK data scaling MOLREP phasing