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Semi-reduced Inhibitor-bound Cyclic Nucleotide Phosphodiesterase from Arabidopsis thaliana
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other semi-reduced CPDase (A. thaliana) [delta 90-115]
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 285 (NH4)2SO4, NaOAc, DTT, 2',3'-cyclic uridine vanadate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 285K
Crystal Properties Matthews coefficient Solvent content 2.1 41.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.14 α = 90 b = 101.14 β = 90 c = 90 γ = 120
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 4 2001-03-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X9B 1.070 NSLS X9B
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 2.4 50 90.3 0.048 15 3 7212 7212 38.4
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 2.4 2.49 95.4 0.466 3
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT semi-reduced CPDase (A. thaliana) [delta 90-115] 2.4 25.29 5960 650 84.2 0.214 0.2189 0.399 0.3946 RANDOM 59.9
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] 0.85 6.95 0.85 -1.71
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 25.2 c_scangle_it 6.01 c_mcangle_it 4.24 c_scbond_it 4.09 c_mcbond_it 2.65 c_angle_deg 2.1 c_improper_angle_d 1.02 c_bond_d 0.013 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 25.2 c_scangle_it 6.01 c_mcangle_it 4.24 c_scbond_it 4.09 c_mcbond_it 2.65 c_angle_deg 2.1 c_improper_angle_d 1.02 c_bond_d 0.013 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1458 Nucleic Acid Atoms Solvent Atoms 94 Heterogen Atoms 62
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling AMoRE phasing CNS refinement