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The Crystal Structure of a Novel, Latent Dihydroorotase from Aquifex Aeolicus at 1.7 A Resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XRF PDB ENTRY 1XRF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 298 ethanol, peg 400, acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.75 54.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 174.201 α = 90 b = 91.235 β = 93.15 c = 61.183 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 93 IMAGE PLATE RIGAKU RAXIS HTC OSMIC MIRRORS 2002-02-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-D 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.609 20 79.2 0.105 4.8 6.5 121022 95834
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.609 1.67 14.5 0.243 2.8 3 1466
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1XRF 1.609 20 121022 90961 4873 77.56 0.1669 0.16688 0.16463 0.1702 0.20794 0.2097 RANDOM 18.931
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] -2.52 0.12 -0.81 3.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.148 r_scangle_it 5.431 r_scbond_it 3.192 r_mcangle_it 1.907 r_angle_refined_deg 1.77 r_mcbond_it 1.102 r_angle_other_deg 0.925 r_nbd_other 0.254 r_symmetry_vdw_refined 0.254 r_symmetry_vdw_other 0.253
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.148 r_scangle_it 5.431 r_scbond_it 3.192 r_mcangle_it 1.907 r_angle_refined_deg 1.77 r_mcbond_it 1.102 r_angle_other_deg 0.925 r_nbd_other 0.254 r_symmetry_vdw_refined 0.254 r_symmetry_vdw_other 0.253 r_nbd_refined 0.232 r_symmetry_hbond_refined 0.232 r_xyhbond_nbd_refined 0.21 r_chiral_restr 0.112 r_nbtor_other 0.088 r_bond_refined_d 0.02 r_gen_planes_refined 0.008 r_gen_planes_other 0.005 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5699 Nucleic Acid Atoms Solvent Atoms 1239 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement CrystalClear data reduction d*TREK data scaling CCP4 phasing