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Crystal structure of Glucose-6-phosphate isomerase (EC 5.3.1.9) (TM1385) from Thermotoga maritima at 1.82 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1B0Z PDB entry 1B0Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 273 NANODROP, 0.23M Li Sulfate, 0.10M Tris-HCl, 0.031M HCl, 43% PEG 400, VAPOR DIFFUSION, SITTING DROP, temperature 273K
Crystal Properties Matthews coefficient Solvent content 2.91 57.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.506 α = 90 b = 125.867 β = 90 c = 245.476 γ = 90
Symmetry Space Group I 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 2005-07-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 1.00000 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 1.82 45.932 99.8 0.052 19.96 7.9 161864 -3 35.51
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) 1.82 1.89 99.9 0.666 2.1
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 1B0Z 1.82 45.932 161863 8195 99.84 0.199 0.197 0.2006 0.237 0.2369 RANDOM 37.431
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] 4.31 -1.89 -2.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.453 r_dihedral_angle_4_deg 18.151 r_dihedral_angle_3_deg 14.371 r_scangle_it 7.229 r_dihedral_angle_1_deg 5.945 r_scbond_it 5.182 r_mcangle_it 2.989 r_mcbond_it 1.962 r_angle_refined_deg 1.607 r_angle_other_deg 0.994
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.453 r_dihedral_angle_4_deg 18.151 r_dihedral_angle_3_deg 14.371 r_scangle_it 7.229 r_dihedral_angle_1_deg 5.945 r_scbond_it 5.182 r_mcangle_it 2.989 r_mcbond_it 1.962 r_angle_refined_deg 1.607 r_angle_other_deg 0.994 r_mcbond_other 0.406 r_symmetry_vdw_other 0.264 r_nbd_refined 0.214 r_nbd_other 0.197 r_symmetry_hbond_refined 0.193 r_nbtor_refined 0.186 r_xyhbond_nbd_refined 0.164 r_symmetry_vdw_refined 0.129 r_chiral_restr 0.097 r_nbtor_other 0.09 r_bond_refined_d 0.018 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10624 Nucleic Acid Atoms Solvent Atoms 613 Heterogen Atoms 100
Software Software Software Name Purpose REFMAC refinement PHENIX refinement MolProbity model building XSCALE data scaling PDB_EXTRACT data extraction MAR345 data collection XDS data reduction MOLREP phasing