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The Crystal Structure of a Protein in the Alkaline Phosphatase Superfamily from Vibrio parahaemolyticus to 1.95A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 289 20% PEG 8000, 0.1M HEPES pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 1.93 36.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.603 α = 90 b = 164.521 β = 109.34 c = 50.929 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 ADSC QUANTUM 315 2009-12-21 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.9794 APS 19-ID
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 1.95 50 98.9 0.105 7.6 3.1 55351
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) 1.95 2.02 98.1 0.481 3.1 5452
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 THROUGHOUT 1.95 40.99 55308 2813 98.85 0.2 0.198 0.1974 0.237 0.2367 RANDOM 37.989
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] -0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.208 r_dihedral_angle_4_deg 17.524 r_dihedral_angle_3_deg 15.288 r_dihedral_angle_1_deg 5.879 r_scangle_it 2.235 r_scbond_it 1.639 r_angle_refined_deg 1.274 r_mcangle_it 0.761 r_mcbond_it 0.45 r_chiral_restr 0.089
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.208 r_dihedral_angle_4_deg 17.524 r_dihedral_angle_3_deg 15.288 r_dihedral_angle_1_deg 5.879 r_scangle_it 2.235 r_scbond_it 1.639 r_angle_refined_deg 1.274 r_mcangle_it 0.761 r_mcbond_it 0.45 r_chiral_restr 0.089 r_bond_refined_d 0.011 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6402 Nucleic Acid Atoms Solvent Atoms 268 Heterogen Atoms 2
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction SBC-Collect data collection HKL-3000 data reduction HKL-3000 data scaling SHELX phasing MLPHARE phasing DM phasing ARP/wARP model building Coot model building