3M5D

Crystal structure of N-acetyl-L-ornithine transcarbamylase K302R mutant complexed with PALAO


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3M4J 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1hanging drop6291Lithium sulfate, Bis-tris, PEG3350, pH 6.0, hanging drop, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.1542.72

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 127.393α = 90
b = 127.393β = 90
c = 127.393γ = 90
Symmetry
Space GroupI 21 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray95IMAGE PLATERIGAGU RAXIS IV2009-12-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU3001.54178

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
12.2501000.0988.71417635
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)
2.22.241000.79113.1879

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3M4J2.245.041758685299.70.2130.1890.222RANDOM35.471
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]
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d22.4
c_scangle_it2.52
c_mcangle_it1.88
c_scbond_it1.87
c_angle_deg1.2
c_mcbond_it1.2
c_bond_d0.005
c_improper_angle_d
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2618
Nucleic Acid Atoms
Solvent Atoms146
Heterogen Atoms24

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACTdata extraction
StructureStudiodata collection
HKL-2000data reduction
CNSphasing