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Crystal structure of choline/ethanolamine kinase family protein (NP_106042.1) from MESORHIZOBIUM LOTI at 2.55 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.8 277 0.2000M NaNO3, 20.0000% PEG-3350, No Buffer pH 6.8, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.63 53.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.07 α = 90 b = 173.62 β = 90 c = 39.93 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 MARMOSAIC 325 mm CCD Flat mirror (vertical focusing) 2008-06-15 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.97882,0.97949,0.91837 SSRL BL11-1
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 2.55 29.566 97.9 0.071 10.09 23913 -3 61.65
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 2.55 2.64 93.3 0.682 1.4
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 2.55 29.566 23862 1222 99.28 0.244 0.242 0.2426 0.284 0.2797 RANDOM 41.477
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] 4.99 -2.99 -2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.183 r_dihedral_angle_4_deg 14.844 r_dihedral_angle_3_deg 14.471 r_scangle_it 5.501 r_scbond_it 4.163 r_dihedral_angle_1_deg 3.885 r_mcangle_it 2.378 r_mcbond_it 1.49 r_angle_refined_deg 1.345 r_angle_other_deg 0.889
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.183 r_dihedral_angle_4_deg 14.844 r_dihedral_angle_3_deg 14.471 r_scangle_it 5.501 r_scbond_it 4.163 r_dihedral_angle_1_deg 3.885 r_mcangle_it 2.378 r_mcbond_it 1.49 r_angle_refined_deg 1.345 r_angle_other_deg 0.889 r_mcbond_other 0.325 r_symmetry_vdw_refined 0.284 r_symmetry_vdw_other 0.244 r_nbd_refined 0.227 r_nbd_other 0.191 r_nbtor_refined 0.186 r_xyhbond_nbd_refined 0.154 r_symmetry_hbond_refined 0.123 r_nbtor_other 0.088 r_chiral_restr 0.077 r_bond_refined_d 0.013 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 4456 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
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