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The crystal structure of PhaZ7 at atomic (1.2 Angstrom) resolution reveals details of the active site and suggests a substrate binding mode
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VTV PDB ENTRY 2VTV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 289 PHAZ7 WAS CRYSTALLIZED IN THE PRESENCE OF PMSF USING THE HANGING DROP VAPOR DIFFUSION METHOD AT 16 C. THE WELL SOLUTION CONSISTED OF 20% W/V PEG3350 AND 0.2 M NA IODIDE AND A 0.1 M PMSF STOCK SOLUTION IN ISOPROPANOL WAS ADDED TO THE WELL TO A FINAL CONCENTRATION OF 10 MM.A 1.5 MICROLITER PROTEIN SOLUTION WAS MIXED WITH AN EQUAL VOLUME OF WELL SOLUTION ON SILICONIZED COVERSLIPS.
Crystal Properties Matthews coefficient Solvent content 2.57 52.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.63 α = 90 b = 140.58 β = 90 c = 56.75 γ = 90
Symmetry Space Group P 21 21 2
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 CCD 2008-03-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 ESRF ID14-2
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 1.2 20 99.9 0.1 11.1 5.9 124737 3.5
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 1.2 1.23 99.9 0.43 3.6 99.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 FREE R-VALUE PDB ENTRY 2VTV 1.2 20 98593 95 0.1392 0.139 0.1379 0.176 0.1713 RANDOM
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]
Coordinate Error Structure Solution Method Refinement High Resolution Refinement Low Resolution 16 3140
RMS Deviations Key Refinement Restraint Deviation s_anti_bump_dis_restr 0.519 s_approx_iso_adps 0.091 s_non_zero_chiral_vol 0.077 s_zero_chiral_vol 0.073 s_similar_adp_cmpnt 0.033 s_from_restr_planes 0.0286 s_angle_d 0.026 s_bond_d 0.011 s_rigid_bond_adp_cmpnt 0.004 s_similar_dist
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2549 Nucleic Acid Atoms Solvent Atoms 563 Heterogen Atoms 29
Software Software Software Name Purpose SHELXL-97 refinement XDS data reduction XDS data scaling PHASER phasing