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Crystal Structure of highly thermostable glycerol kinase from a hyperthermophilic archaeon
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GLA PDB ENTRY 1GLA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 30% PEG400, 0.1M Tris, 0.2M MgCl2, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.7 54.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 217.477 α = 90 b = 217.477 β = 90 c = 66.479 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 Bruker DIP-6040 2006-05-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9 SPring-8 BL44XU
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 50 98.2 0.081 17.2 45951
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 2.49 94 0.472 1.4
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1GLA 2.4 41.1 42820 2274 98.17 0.17803 0.17402 0.173 0.25493 0.255 RANDOM 46.957
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] -0.01 -0.01 -0.01 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.516 r_dihedral_angle_4_deg 25.553 r_dihedral_angle_3_deg 22.079 r_dihedral_angle_1_deg 9.222 r_scangle_it 6.222 r_scbond_it 3.947 r_mcangle_it 2.761 r_angle_refined_deg 2.567 r_mcbond_it 1.79 r_symmetry_vdw_refined 0.368
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.516 r_dihedral_angle_4_deg 25.553 r_dihedral_angle_3_deg 22.079 r_dihedral_angle_1_deg 9.222 r_scangle_it 6.222 r_scbond_it 3.947 r_mcangle_it 2.761 r_angle_refined_deg 2.567 r_mcbond_it 1.79 r_symmetry_vdw_refined 0.368 r_nbtor_refined 0.325 r_symmetry_hbond_refined 0.319 r_nbd_refined 0.246 r_chiral_restr 0.234 r_xyhbond_nbd_refined 0.2 r_bond_refined_d 0.03 r_gen_planes_refined 0.011 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7842 Nucleic Acid Atoms Solvent Atoms 133 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing