3SW6

Crystal structure of Methanothermobacter thermautotrophicus orotidine 5'-monophosphate decarboxylase covalently modified by 5-fluoro-6-azido-UMP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1DV7 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.2293Trisodium Citrate, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.0740.63

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.118α = 90
b = 103.37β = 90
c = 73.92γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152007-02-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 14-BM-C0.90020APS14-BM-C

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
11.55099.60.04913.45.63588034615
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)
11.51.5399.20.3743.5751770

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 REPLACEMENTTHROUGHOUT1DV71.55034062179299.590.162360.160970.18909RANDOM15.78
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]
0.32-0.540.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.745
r_dihedral_angle_4_deg19.519
r_dihedral_angle_3_deg12.902
r_dihedral_angle_1_deg5.419
r_scangle_it3.993
r_scbond_it2.362
r_mcangle_it1.505
r_angle_refined_deg1.46
r_mcbond_it0.833
r_chiral_restr0.093
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.745
r_dihedral_angle_4_deg19.519
r_dihedral_angle_3_deg12.902
r_dihedral_angle_1_deg5.419
r_scangle_it3.993
r_scbond_it2.362
r_mcangle_it1.505
r_angle_refined_deg1.46
r_mcbond_it0.833
r_chiral_restr0.093
r_gen_planes_refined0.011
r_bond_refined_d0.01
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1622
Nucleic Acid Atoms
Solvent Atoms127
Heterogen Atoms22

Software

Software
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling