1RXY

E. coli uridine phosphorylase: type-B native


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1LGGTYPE-A NATIVE (1LGG)

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5289TRIS HCL, PEG4000, POTASSIUM ACETATE, pH 7.50, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.2544.85

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 152.928α = 90
b = 152.928β = 90
c = 50.864γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDADSC QUANTUM 41999-04-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X26C1.10NSLSX26C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.716.5499.90.0539.75.4487154871521.544
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.71.7999.90.3372.25.17095

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTTYPE-A NATIVE (1LGG)1.716.14622446224247899.980.130020.128190.16442RANDOM12.299
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]
0.030.020.03-0.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.944
r_scangle_it2.334
r_scbond_it1.562
r_angle_refined_deg1.547
r_angle_other_deg1.264
r_mcangle_it1.109
r_mcbond_it0.683
r_symmetry_vdw_other0.312
r_nbd_other0.235
r_nbd_refined0.214
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.944
r_scangle_it2.334
r_scbond_it1.562
r_angle_refined_deg1.547
r_angle_other_deg1.264
r_mcangle_it1.109
r_mcbond_it0.683
r_symmetry_vdw_other0.312
r_nbd_other0.235
r_nbd_refined0.214
r_symmetry_hbond_refined0.209
r_chiral_restr0.168
r_xyhbond_nbd_refined0.154
r_symmetry_vdw_refined0.098
r_nbtor_other0.078
r_metal_ion_refined0.031
r_bond_refined_d0.016
r_gen_planes_refined0.006
r_gen_planes_other0.005
r_bond_other_d0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3703
Nucleic Acid Atoms
Solvent Atoms415
Heterogen Atoms28

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
REFMACrefinement
CCP4data scaling