☰ Navigation Tabs
Crystal structure of Glycerate kinase (EC 2.7.1.31) (tm1585) from THERMOTOGA MARITIMA at 2.70 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION,SITTING DROP,NANODROP 9 293 65% MPD, 0.1M bicine pH 9.0 , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.6 52.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.954 α = 90 b = 85.169 β = 90 c = 172.507 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 ADSC QUANTUM 315 2002-07-07 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.904965, 0.979126 SSRL BL9-2
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 2.52 48.11 75.1 0.072 0.072 7.71 2.89 26442
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 2.52 2.61 30.2 0.234 0.234 2.59
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 (All) 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 2.53 48.11 25084 1314 84.37 0.185 0.1848 0.182 0.1916 0.246 0.2911 RANDOM 27.296
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] -0.29 -1.01 1.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.936 r_dihedral_angle_4_deg 20.343 r_dihedral_angle_3_deg 16.219 r_dihedral_angle_1_deg 5.855 r_scangle_it 5.613 r_scbond_it 3.828 r_mcangle_it 1.834 r_angle_refined_deg 1.379 r_mcbond_it 1.18 r_angle_other_deg 0.821
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.936 r_dihedral_angle_4_deg 20.343 r_dihedral_angle_3_deg 16.219 r_dihedral_angle_1_deg 5.855 r_scangle_it 5.613 r_scbond_it 3.828 r_mcangle_it 1.834 r_angle_refined_deg 1.379 r_mcbond_it 1.18 r_angle_other_deg 0.821 r_mcbond_other 0.379 r_symmetry_vdw_refined 0.316 r_symmetry_vdw_other 0.248 r_nbd_refined 0.207 r_nbtor_refined 0.17 r_nbd_other 0.169 r_xyhbond_nbd_refined 0.16 r_symmetry_hbond_refined 0.119 r_nbtor_other 0.083 r_chiral_restr 0.072 r_bond_refined_d 0.013 r_gen_planes_refined 0.004 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6147 Nucleic Acid Atoms Solvent Atoms 97 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction SHELX phasing autoSHARP phasing