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X-Ray Structure of Adenosine 5'-Monophosphate Deaminase from Arabidopsis Thaliana in Complex with Coformycin 5'-Phosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other RABBIT AMPD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.6 295 8 MG/ML PROTEIN,
0.40 M MONOAMMONIUM DIHYDROGEN PHOSPHATE,
0.10 M TRI-SODIUM CITRATE, 10% (V/V) ETHANOL, vapor diffusion, hanging drop, temperature 295K, pH 5.60
Crystal Properties Matthews coefficient Solvent content 3.28 62.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 131.325 α = 90 b = 131.325 β = 90 c = 208.254 γ = 120
Symmetry Space Group P 62 2 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 MARMOSAIC 300 mm CCD HORIZONTAL SAGITALLY FOCUSING 2ND BENT MONOCHROMATOR CRYSTAL, VERTICAL BENT FOCUSING MIRROR 2005-03-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID APS 22-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 3.34 50 99.6 0.06 22.579 6.1 16001
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 3.34 3.42 99.5 0.489 3.922 5.7
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 RABBIT AMPD 3.34 49.91 15038 741 93.8 0.237 0.237 0.228 0.323 0.318 RANDOM 73.5
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] 10.914 -1.407 10.914 -21.828
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 24.8 c_angle_deg 2.4 c_improper_angle_d 1.48 c_bond_d 0.016 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 24.8 c_angle_deg 2.4 c_improper_angle_d 1.48 c_bond_d 0.016 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 c_mcbond_it c_mcangle_it c_scbond_it c_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5050 Nucleic Acid Atoms Solvent Atoms 24 Heterogen Atoms 30
Software Software Software Name Purpose CNS refinement SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction DENZO data reduction