3L0N

Human orotidyl-5'-monophosphate decarboxylase in complex with 6-mercapto-UMP


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP83000.1M Tris-HCl pH 8.0, 1.8M (NH4)2SO4, VAPOR DIFFUSION, SITTING DROP, temperature 300.0K
Crystal Properties
Matthews coefficientSolvent content
2.4449.67

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 69.644α = 90
b = 62.165β = 113.99
c = 69.935γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plate2007-10-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.7434.6597.60.07812.64.95387526.463
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.751.79800.5751.42.62192

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.7434.6551149271496.190.181820.180470.20737RANDOM22.011
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]
-5.3514.96-14.2319.57
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.621
r_dihedral_angle_4_deg17.245
r_dihedral_angle_3_deg14.11
r_dihedral_angle_1_deg6.398
r_angle_refined_deg1.61
r_angle_other_deg0.985
r_chiral_restr0.092
r_mcbond_it0.026
r_mcbond_other0.021
r_bond_refined_d0.017
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.621
r_dihedral_angle_4_deg17.245
r_dihedral_angle_3_deg14.11
r_dihedral_angle_1_deg6.398
r_angle_refined_deg1.61
r_angle_other_deg0.985
r_chiral_restr0.092
r_mcbond_it0.026
r_mcbond_other0.021
r_bond_refined_d0.017
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_it
r_scbond_it
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3944
Nucleic Acid Atoms
Solvent Atoms262
Heterogen Atoms44

Software

Software
Software NamePurpose
REFMACrefinement