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Crystal structure of glycerophosphodiester phosphodiesterase from Thermococcus kodakarensis KOD1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OTD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 30%(w/v) PEG4000, 0.2M Magnesium chloride hexahydrate, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.17 43.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.724 α = 90 b = 132.034 β = 90 c = 171.639 γ = 90
Symmetry Space Group P 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 BRUKER SMART 6500 2012-07-04 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) 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 1.9 50 99.8 0.142 0.142 23.493 13.6 79998 -3
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 1.9 1.93 100 0.558 14.4 3943
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 (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 MOLECULAR REPLACEMENT THROUGHOUT 2otd 1.9 50 79606 3998 99.18 0.197 0.197 0.1942 0.1996 0.2499 0.2549 RANDOM 30.063
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] 1.08 1.91 -2.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.312 r_dihedral_angle_4_deg 18.111 r_dihedral_angle_3_deg 14.998 r_dihedral_angle_1_deg 7.232 r_scangle_it 5.973 r_scbond_it 3.906 r_mcangle_it 2.335 r_mcbond_it 1.507 r_angle_refined_deg 0.978 r_chiral_restr 0.089
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.312 r_dihedral_angle_4_deg 18.111 r_dihedral_angle_3_deg 14.998 r_dihedral_angle_1_deg 7.232 r_scangle_it 5.973 r_scbond_it 3.906 r_mcangle_it 2.335 r_mcbond_it 1.507 r_angle_refined_deg 0.978 r_chiral_restr 0.089 r_gen_planes_refined 0.015 r_bond_refined_d 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8016 Nucleic Acid Atoms Solvent Atoms 693 Heterogen Atoms 4
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection BALBES phasing