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Crystal structure of 6-phosphogluconolactonase (TM1154) from Thermotoga maritima at 1.70A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PBT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION,SITTING DROP,NANODROP 277 0.2M (NH4)2HCitrate, 20% PEG-3350 , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 1.93 35.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.733 α = 90 b = 75.146 β = 90 c = 148.443 γ = 90
Symmetry Space Group C 2 2 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 2004-04-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 ALS 8.3.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.55 50 79.46 0.075 16.59 3.86 24729 23.98
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.55 1.61 26.04 0.325 2.93 2.57 798
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 1PBT 1.55 37.11 23466 1262 79.32 0.16717 0.16523 0.1775 0.20395 0.2174 RANDOM 22.367
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] -0.31 2.44 -2.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.484 r_dihedral_angle_4_deg 16.694 r_dihedral_angle_3_deg 11.733 r_dihedral_angle_1_deg 6.249 r_scangle_it 3.979 r_scbond_it 2.733 r_angle_refined_deg 1.62 r_mcangle_it 1.535 r_mcbond_it 1.151 r_angle_other_deg 0.876
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.484 r_dihedral_angle_4_deg 16.694 r_dihedral_angle_3_deg 11.733 r_dihedral_angle_1_deg 6.249 r_scangle_it 3.979 r_scbond_it 2.733 r_angle_refined_deg 1.62 r_mcangle_it 1.535 r_mcbond_it 1.151 r_angle_other_deg 0.876 r_symmetry_vdw_other 0.364 r_mcbond_other 0.327 r_symmetry_vdw_refined 0.294 r_nbd_refined 0.218 r_symmetry_hbond_refined 0.194 r_nbd_other 0.184 r_xyhbond_nbd_refined 0.133 r_chiral_restr 0.115 r_nbtor_other 0.083 r_bond_refined_d 0.018 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1766 Nucleic Acid Atoms Solvent Atoms 167 Heterogen Atoms 13
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement