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Crystal structure of putative phosphoglycolate phosphatase (YP_619066.1) from Lactobacillus delbrueckii subsp. bulgaricus ATCC BAA-365 at 1.51 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION,SITTING DROP,NANODROP 6.5 277 0.2M NaOAc, 30.0% PEG-8000, 0.1M Cacodylate pH 6.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.18 43.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.636 α = 90 b = 38.695 β = 98.09 c = 103.583 γ = 90
Symmetry Space Group P 1 21 1
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 2006-06-04 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.91837, 0.97939 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 1.51 47.727 95.8 0.101 8.75 3.61 72271 19.143
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 1.51 1.56 82.6 0.537 2.1 2.77 5575
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 1.51 47.727 72257 3644 99.17 0.158 0.158 0.157 0.165 0.19 0.1959 RANDOM 11.423
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] -0.07 0.19 0.17 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.547 r_dihedral_angle_4_deg 15.444 r_dihedral_angle_3_deg 13.063 r_scangle_it 6.563 r_dihedral_angle_1_deg 5.487 r_scbond_it 4.43 r_mcangle_it 2.632 r_mcbond_it 1.707 r_angle_refined_deg 1.592 r_angle_other_deg 0.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.547 r_dihedral_angle_4_deg 15.444 r_dihedral_angle_3_deg 13.063 r_scangle_it 6.563 r_dihedral_angle_1_deg 5.487 r_scbond_it 4.43 r_mcangle_it 2.632 r_mcbond_it 1.707 r_angle_refined_deg 1.592 r_angle_other_deg 0.99 r_mcbond_other 0.532 r_symmetry_vdw_other 0.289 r_nbd_refined 0.229 r_metal_ion_refined 0.208 r_nbd_other 0.196 r_nbtor_refined 0.182 r_symmetry_hbond_refined 0.177 r_symmetry_vdw_refined 0.176 r_xyhbond_nbd_refined 0.151 r_chiral_restr 0.093 r_nbtor_other 0.086 r_bond_refined_d 0.017 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3675 Nucleic Acid Atoms Solvent Atoms 637 Heterogen Atoms 81
Software Software Software Name Purpose MolProbity model building REFMAC refinement XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction SHELXD phasing autoSHARP phasing