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Crystal Structure of a putative glycerophosphodiester phosphodiesterase from Galdieria sulphuraria
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 Protein Solution (10 MG/ML protein, 0.050 M sodium chloride, 0.0031 M sodium azide, 0.0003 M TCEP, 0.005 M Bis Tris pH 7.0) mixed in a 1:1 ratio with the Well Solution (0.90 M lithium sulfate, 0.10 M sodium succinate pH 4), Cryoprotected with: well solution supplemented with up to 20% glycerol, vapor diffusion, hanging drop, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.7 53.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.427 α = 90 b = 102.427 β = 90 c = 51.709 γ = 120
Symmetry Space Group P 31 2 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 300 mm CCD Adjustable focusing mirrors in K-B geometry 2006-11-08 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 0.97923, 0.96400 APS 23-ID-D
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 2.8 36.387 97.4 0.099 15.064 12.7 7690
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 2.8 2.9 82.5 0.197 4.527 4.6 631
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 (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 2.806 36.387 7678 352 97.412 0.195 0.192 0.2058 0.255 0.2596 RANDOM 17.983
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] 1.506 0.753 1.506 -2.258
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.546 r_dihedral_angle_3_deg 20.807 r_dihedral_angle_4_deg 19.714 r_dihedral_angle_1_deg 8.242 r_scangle_it 2.251 r_angle_refined_deg 1.486 r_scbond_it 1.363 r_mcangle_it 0.844 r_mcbond_it 0.46 r_nbtor_refined 0.316
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.546 r_dihedral_angle_3_deg 20.807 r_dihedral_angle_4_deg 19.714 r_dihedral_angle_1_deg 8.242 r_scangle_it 2.251 r_angle_refined_deg 1.486 r_scbond_it 1.363 r_mcangle_it 0.844 r_mcbond_it 0.46 r_nbtor_refined 0.316 r_nbd_refined 0.235 r_symmetry_vdw_refined 0.235 r_symmetry_hbond_refined 0.171 r_xyhbond_nbd_refined 0.15 r_chiral_restr 0.102 r_bond_refined_d 0.014 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2045 Nucleic Acid Atoms Solvent Atoms 1 Heterogen Atoms 15
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling SHARP phasing DM phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction