1VQT

Crystal structure of Orotidine 5'-phosphate decarboxylase (TM0332) from Thermotoga maritima at 2.00 A resolution


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION,SITTING DROP,NANODROP6.527712.0% PEG-20000, 0.1M MES pH 6.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.5852.04

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 70.688α = 90
b = 85.55β = 130.2
c = 48.725γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC2004-09-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.2.1ALS8.2.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.99999.470.06628.054.811741055.68
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.91.9395.321.343.41836

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 REPLACEMENTTHROUGHOUT1EIX2271418075899.610.183430.181390.22088RANDOM58.589
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]
2.07-1.36-3.3-0.53
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.102
r_dihedral_angle_4_deg19.956
r_dihedral_angle_3_deg14.754
r_dihedral_angle_1_deg6.244
r_scangle_it3.323
r_scbond_it2.256
r_angle_refined_deg1.671
r_mcangle_it1.476
r_mcbond_it0.995
r_angle_other_deg0.839
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.102
r_dihedral_angle_4_deg19.956
r_dihedral_angle_3_deg14.754
r_dihedral_angle_1_deg6.244
r_scangle_it3.323
r_scbond_it2.256
r_angle_refined_deg1.671
r_mcangle_it1.476
r_mcbond_it0.995
r_angle_other_deg0.839
r_symmetry_vdw_refined0.494
r_mcbond_other0.257
r_symmetry_hbond_refined0.233
r_nbd_refined0.213
r_nbtor_refined0.185
r_nbd_other0.183
r_symmetry_vdw_other0.178
r_xyhbond_nbd_refined0.157
r_chiral_restr0.103
r_nbtor_other0.09
r_bond_refined_d0.018
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1457
Nucleic Acid Atoms
Solvent Atoms61
Heterogen Atoms36

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement