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Structure of OHCU decarboxylase in complex with allantoin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2O70
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8.5 278 20% (v/v) EtOH, 100mM TrisHCl, pH 8.5, VAPOR DIFFUSION, temperature 278K
Crystal Properties Matthews coefficient Solvent content 2.64 53.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.212 α = 90 b = 102.212 β = 90 c = 103.868 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 315 2006-09-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.98 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 1.8 88.39 93 0.089 9.5 2.7 104588 104588
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 1.8 1.9 72.7 0.45 1.7 2 11935
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) 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 FOURIER SYNTHESIS THROUGHOUT 2O70 1.8 83 0.45 99340 99340 5205 92.96 0.21876 0.21876 0.21703 0.2164 0.25151 0.2486 RANDOM 23.034
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] 0.02 0.01 0.02 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.302 r_dihedral_angle_4_deg 18.894 r_dihedral_angle_3_deg 14.485 r_dihedral_angle_1_deg 5.016 r_scangle_it 1.914 r_mcangle_it 1.668 r_scbond_it 1.256 r_angle_refined_deg 1.199 r_mcbond_it 1.102 r_nbtor_refined 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.302 r_dihedral_angle_4_deg 18.894 r_dihedral_angle_3_deg 14.485 r_dihedral_angle_1_deg 5.016 r_scangle_it 1.914 r_mcangle_it 1.668 r_scbond_it 1.256 r_angle_refined_deg 1.199 r_mcbond_it 1.102 r_nbtor_refined 0.31 r_nbd_refined 0.232 r_symmetry_hbond_refined 0.228 r_xyhbond_nbd_refined 0.206 r_symmetry_vdw_refined 0.201 r_chiral_restr 0.081 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 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_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7895 Nucleic Acid Atoms Solvent Atoms 550 Heterogen Atoms 66
Software Software Software Name Purpose REFMAC refinement ADSC data collection MOSFLM data reduction CCP4 data scaling