3SEC

Crystal structure of Methanothermobacter thermautotrophicus orotidine 5'-monophosphate decarboxylase complexed with pyrazofurin monophosphate


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.8293Trisodium Citrate, Dioxane, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.0840.73

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.244α = 90
b = 103.574β = 90
c = 73.739γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152006-08-07MSINGLE 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
11.75099.90.08411.79.624704
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)
11.71.7399.70.4894.437.4

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 REPLACEMENTTHROUGHOUT1DV71.7502402764899.660.156610.155840.18683RANDOM17.911
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]
0.4-0.750.35
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.238
r_dihedral_angle_4_deg18.547
r_dihedral_angle_3_deg15.164
r_dihedral_angle_1_deg5.687
r_scangle_it3.857
r_scbond_it2.508
r_angle_refined_deg1.564
r_mcangle_it1.476
r_mcbond_it0.963
r_nbtor_refined0.313
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.238
r_dihedral_angle_4_deg18.547
r_dihedral_angle_3_deg15.164
r_dihedral_angle_1_deg5.687
r_scangle_it3.857
r_scbond_it2.508
r_angle_refined_deg1.564
r_mcangle_it1.476
r_mcbond_it0.963
r_nbtor_refined0.313
r_nbd_refined0.227
r_symmetry_vdw_refined0.147
r_xyhbond_nbd_refined0.121
r_chiral_restr0.103
r_symmetry_hbond_refined0.1
r_bond_refined_d0.011
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1622
Nucleic Acid Atoms
Solvent Atoms146
Heterogen Atoms28

Software

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