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Crystal structure of adenine phosphoribosyltransferase from Rhodothermus marinus DSM 4252, NYSGRC Target 029775.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DY0 PDB ENTRY 2DY0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 298 0.2 M calcium chloride, 0.1 M HEPES:NAOH, pH 7.5, 30%
PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.09 41.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.214 α = 87.3 b = 64.609 β = 77.23 c = 73.148 γ = 85.37
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 RAYONIX MX225HE 2013-07-18 SAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.9791 APS 31-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 1.4 50 95.9 0.07 12.7 3.8 135383
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 1.4 1.42 93 0.667 3.7 6539
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 2DY0 1.4 20 135182 6751 95.89 0.185 0.1837 0.1834 0.2095 0.209 RANDOM 22.5222
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] 1.17 -0.73 1.29 -0.88 -0.37 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.536 r_dihedral_angle_3_deg 13.779 r_dihedral_angle_4_deg 13.105 r_dihedral_angle_1_deg 6.183 r_mcangle_it 2.091 r_scbond_it 1.768 r_angle_refined_deg 1.406 r_mcbond_it 1.183 r_chiral_restr 0.089 r_bond_refined_d 0.008
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.536 r_dihedral_angle_3_deg 13.779 r_dihedral_angle_4_deg 13.105 r_dihedral_angle_1_deg 6.183 r_mcangle_it 2.091 r_scbond_it 1.768 r_angle_refined_deg 1.406 r_mcbond_it 1.183 r_chiral_restr 0.089 r_bond_refined_d 0.008 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5383 Nucleic Acid Atoms Solvent Atoms 602 Heterogen Atoms 96
Software Software Software Name Purpose SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction