4FJS | pdb_00004fjs

Crystal structure of ureidoglycolate dehydrogenase enzyme in apo form


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1XRH 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1EVAPORATION60.1M MES, 4.0M NACL, pH 6.0, EVAPORATION
Crystal Properties
Matthews coefficientSolvent content
2.5351.37

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 162.76α = 90
b = 162.76β = 90
c = 61.45γ = 90
Symmetry
Space GroupP 42 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2010-05-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPAL/PLS BEAMLINE 4APAL/PLS4A

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
11.75099.90.1236.723.2463522
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)
12.52.5499.90.60616.9

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)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)Mean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENT1XHR2.1349.181.34463052000990.2230.2220.250.240.27
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]
1.3211.321-2.6419
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d17.15
f_angle_d1.113
f_chiral_restr0.079
f_bond_d0.009
f_plane_restr0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4959
Nucleic Acid Atoms
Solvent Atoms500
Heterogen Atoms

Software

Software
Software NamePurpose
PHENIXrefinement
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing