2ZZ5

Orotidine Monophosphate Deacarboxylase D70A/K72A double mutant from M. thermoautotrophicum complexed with 6- cyano-UMP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2E6Y 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION2981.2-1.36M Sodium Citrate, 5% dioxiane, pH 6.0-8.5, VAPOR DIFFUSION, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
1.9536.95

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.556α = 90
b = 64.359β = 115.52
c = 61.539γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayCCDADSC QUANTUM 315default2006-12-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 14-BM-CAPS14-BM-C

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
11.5610083.90.0839.93.650081
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.561.5930.20.431.4

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 REPLACEMENTTHROUGHOUT2E6Y1.5655.5647506254483.870.161180.159760.18679RANDOM18.72
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]
-1.21-1.050.220.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.8
r_dihedral_angle_4_deg17.485
r_dihedral_angle_3_deg14.492
r_dihedral_angle_1_deg6.033
r_scangle_it5.372
r_scbond_it3.321
r_mcangle_it1.855
r_angle_refined_deg1.793
r_mcbond_it1.258
r_nbtor_refined0.311
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.8
r_dihedral_angle_4_deg17.485
r_dihedral_angle_3_deg14.492
r_dihedral_angle_1_deg6.033
r_scangle_it5.372
r_scbond_it3.321
r_mcangle_it1.855
r_angle_refined_deg1.793
r_mcbond_it1.258
r_nbtor_refined0.311
r_nbd_refined0.207
r_symmetry_vdw_refined0.171
r_chiral_restr0.128
r_xyhbond_nbd_refined0.124
r_symmetry_hbond_refined0.114
r_bond_refined_d0.021
r_gen_planes_refined0.009
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3220
Nucleic Acid Atoms
Solvent Atoms199
Heterogen Atoms46

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CCP4phasing