☰ Navigation Tabs
Human orotidine 5'-phosphate decarboxylase domain of uridine monophospate synthetase (UMPS) in complex with its product UMP.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2JGY PDB ENTRY 2JGY
Crystallization Crystal Properties Matthews coefficient Solvent content 2.65 53.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.103 α = 90 b = 77.853 β = 90 c = 153.209 γ = 90
Symmetry Space Group P 21 21 21
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 2007-02-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 ESRF ID29
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 2 20 99.9 0.07 35.6 14.1 49400
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 2 2.11 100 0.21 12.6 14.4
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 PDB ENTRY 2JGY 2 19.64 46851 2482 100 0.155 0.153 0.1599 0.188 0.1947 RANDOM 17.42
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] -0.49 1.59 -1.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.914 r_dihedral_angle_3_deg 13.311 r_dihedral_angle_4_deg 12.577 r_dihedral_angle_1_deg 6.016 r_scangle_it 3.568 r_scbond_it 2.637 r_mcangle_it 1.59 r_mcbond_it 1.444 r_angle_refined_deg 1.338 r_angle_other_deg 0.949
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.914 r_dihedral_angle_3_deg 13.311 r_dihedral_angle_4_deg 12.577 r_dihedral_angle_1_deg 6.016 r_scangle_it 3.568 r_scbond_it 2.637 r_mcangle_it 1.59 r_mcbond_it 1.444 r_angle_refined_deg 1.338 r_angle_other_deg 0.949 r_symmetry_vdw_other 0.316 r_symmetry_vdw_refined 0.209 r_nbd_refined 0.2 r_nbd_other 0.193 r_xyhbond_nbd_refined 0.176 r_symmetry_hbond_refined 0.17 r_nbtor_refined 0.166 r_nbtor_other 0.083 r_chiral_restr 0.078 r_bond_refined_d 0.012 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other 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 3974 Nucleic Acid Atoms Solvent Atoms 574 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing