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Crystal structure of a HAD-like phosphatase from Enterococcus faecalis V583
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YDF PDB entry 1YDF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 Tris HCL, mono-Ammonium dihydrogen Phosphate, PEG3350, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.5 65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.628 α = 90 b = 126.114 β = 90 c = 112.634 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 QUANTUM 315 mirrors 2005-01-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 0.97 NSLS X25
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 50 100 0.1 6.5 7.2 21058 21058 42
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 2.93 100 0.5 7.4 2575
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 PDB entry 1YDF 2.8 47.12 19963 1967 95.1 0.219 0.219 0.2238 0.28 0.2762 RANDOM 33.4
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] 14.61 -10.61 -4
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.8 c_scangle_it 3.05 c_mcangle_it 2.18 c_scbond_it 1.98 c_angle_deg 1.4 c_mcbond_it 1.27 c_improper_angle_d 0.92 c_bond_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3964 Nucleic Acid Atoms Solvent Atoms 172 Heterogen Atoms 20
Software Software Software Name Purpose CNS refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing