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Crystal structure of red kidney bean purple acid phosphatase in complex with adenosine diphosphate metavanadate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4DHL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4 291.15 2.3 M ammonium sulfate, 0.1 M sodium acetate, pH 4.0
Crystal Properties Matthews coefficient Solvent content 3.43 64.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 126.052 α = 90 b = 126.052 β = 90 c = 295.149 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 ADSC QUANTUM 210r 2011-03-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX1 0.9 Australian Synchrotron MX1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim I (All) CC (Half) 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 2.2 19.9 82 0.068 0.994 8.3 5.4 112252 28.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.225 84.9 0.45 0.585 1.8 3.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4DHL 2.2 19.9 0.3 112059 5649 81.13 0.1654 0.1621 0.1625 0.2268 0.2264 29.91
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.7933 f_angle_d 0.9179 f_chiral_restr 0.0554 f_bond_d 0.0074 f_plane_restr 0.0053
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13971 Nucleic Acid Atoms Solvent Atoms 1331 Heterogen Atoms 736
Software Software Software Name Purpose PHENIX refinement XDS data reduction SCALA data scaling PHASER phasing Blu-Ice data collection