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Crystal structure of a pyrimidine degrading enzyme from Drosophila melanogaster
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4.2 PEG 3350, PHOSPHATE/CITRATE PH 4.2, NACL
Crystal Properties Matthews coefficient Solvent content 2.97 58.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 278.863 α = 90 b = 95.048 β = 125.82 c = 199.312 γ = 90
Symmetry Space Group C 1 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 CCD M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 ESRF ID23-1
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 3.3 50 86 0.17 6.4 2.4 54793 2
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 3.3 3.48 81.2 0.38 2.1 2.4
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 NONE 3.3 30 51958 2764 85.6 0.229 0.226 0.229 0.282 0.2815 RANDOM 41.37
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] 4.01 2.58 0.48 -1.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.902 r_dihedral_angle_3_deg 21.024 r_dihedral_angle_4_deg 19.405 r_dihedral_angle_1_deg 6.914 r_angle_refined_deg 1.255 r_nbtor_refined 0.308 r_symmetry_vdw_refined 0.238 r_nbd_refined 0.214 r_xyhbond_nbd_refined 0.153 r_chiral_restr 0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.902 r_dihedral_angle_3_deg 21.024 r_dihedral_angle_4_deg 19.405 r_dihedral_angle_1_deg 6.914 r_angle_refined_deg 1.255 r_nbtor_refined 0.308 r_symmetry_vdw_refined 0.238 r_nbd_refined 0.214 r_xyhbond_nbd_refined 0.153 r_chiral_restr 0.09 r_symmetry_hbond_refined 0.026 r_bond_refined_d 0.01 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 23681 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing