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Crystal structure of a putative phosphomethylpyrimidine kinase (BT_4458) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 2.10 A resolution (rhombohedral form)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 293 35.00% 2-methyl-2,4-pentanediol, 0.20M lithium sulfate, 0.1M MES pH 6.0, Additive: 0.001M zinc chloride, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.86 57.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 161.627 α = 90 b = 161.627 β = 90 c = 76.138 γ = 120
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 mirror (vertical focusing) 2009-07-09 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.91837,0.97916,0.97871 SSRL BL11-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.1 29.591 100 0.137 0.137 10.7 5.7 22278 28.253
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.15 100 0.838 0.838 0.9 5.7 1645
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 MAD THROUGHOUT 2.1 29.591 22278 1137 99.95 0.173 0.171 0.1828 0.21 0.2172 RANDOM 23.496
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] -1.79 -0.89 -1.79 2.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.374 r_dihedral_angle_4_deg 20.543 r_dihedral_angle_3_deg 14.497 r_dihedral_angle_1_deg 6.686 r_scangle_it 3.698 r_scbond_it 2.488 r_angle_refined_deg 1.615 r_mcangle_it 1.396 r_angle_other_deg 0.941 r_mcbond_it 0.759
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.374 r_dihedral_angle_4_deg 20.543 r_dihedral_angle_3_deg 14.497 r_dihedral_angle_1_deg 6.686 r_scangle_it 3.698 r_scbond_it 2.488 r_angle_refined_deg 1.615 r_mcangle_it 1.396 r_angle_other_deg 0.941 r_mcbond_it 0.759 r_mcbond_other 0.194 r_chiral_restr 0.096 r_bond_refined_d 0.017 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2257 Nucleic Acid Atoms Solvent Atoms 124 Heterogen Atoms 51
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SHELX phasing MolProbity model building SCALA data scaling PDB_EXTRACT data extraction MOSFLM data reduction autoSHARP phasing SHELXD phasing