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Crystal structure of a putative phosphomethylpyrimidine kinase (BT_4458) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 2.00 A resolution (orthorhombic form with pyridoxal)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 277 20.00% polyethylene glycol 3000, 0.20M sodium chloride, 0.1M HEPES pH 7.5, Additive: 0.001 M pyridoxal, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.32 46.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.723 α = 90 b = 138.368 β = 90 c = 143.539 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 100 CCD MARMOSAIC 325 mm CCD Flat collimating mirror, toroid focusing mirror 2009-07-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 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 29.814 98.3 0.048 12.12 125843 -3 30.527
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 2.07 97.5 0.554 1.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 2 29.814 125765 6306 99.57 0.169 0.167 0.1816 0.206 0.2153 RANDOM 21.723
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] -0.63 0.19 0.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.022 r_dihedral_angle_4_deg 20.251 r_dihedral_angle_3_deg 13.841 r_dihedral_angle_1_deg 5.943 r_scangle_it 3.611 r_scbond_it 2.412 r_angle_refined_deg 1.622 r_mcangle_it 1.397 r_angle_other_deg 0.977 r_mcbond_it 0.793
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.022 r_dihedral_angle_4_deg 20.251 r_dihedral_angle_3_deg 13.841 r_dihedral_angle_1_deg 5.943 r_scangle_it 3.611 r_scbond_it 2.412 r_angle_refined_deg 1.622 r_mcangle_it 1.397 r_angle_other_deg 0.977 r_mcbond_it 0.793 r_mcbond_other 0.262 r_chiral_restr 0.098 r_bond_refined_d 0.018 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13632 Nucleic Acid Atoms Solvent Atoms 1022 Heterogen Atoms 76
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SHELX phasing MolProbity model building XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction SHELXD phasing autoSHARP phasing