2ZZ2

Orotidine Monophosphate Decarboxylase K72A mutant from M. thermoautotrophicum complexed with 6-cyano-UMP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1X1Z 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION1.2-1.36M Sodium Citrate, 5% dioxiane, pH 6.0-8.5, VAPOR DIFFUSION
Crystal Properties
Matthews coefficientSolvent content
2.0339.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.086α = 90
b = 73.819β = 119.3
c = 59.323γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayCCDMAR CCD 165 mmdefault2004-03-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 14-ID-B1.0332APS14-ID-B

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
11.5310095.60.05522.16251814
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)
11.531.560.2992.8

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT1x1z1.5351.9959403309195.490.160850.159470.1873same flag with 1x1z14.179
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]
0.04-0.230.26-0.53
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.899
r_dihedral_angle_4_deg20.019
r_dihedral_angle_3_deg11.696
r_dihedral_angle_1_deg5.465
r_scangle_it4.736
r_scbond_it2.931
r_angle_refined_deg1.646
r_mcangle_it1.62
r_mcbond_it1.133
r_nbtor_refined0.313
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.899
r_dihedral_angle_4_deg20.019
r_dihedral_angle_3_deg11.696
r_dihedral_angle_1_deg5.465
r_scangle_it4.736
r_scbond_it2.931
r_angle_refined_deg1.646
r_mcangle_it1.62
r_mcbond_it1.133
r_nbtor_refined0.313
r_symmetry_vdw_refined0.218
r_nbd_refined0.207
r_xyhbond_nbd_refined0.125
r_symmetry_hbond_refined0.121
r_chiral_restr0.111
r_bond_refined_d0.016
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 Atoms3252
Nucleic Acid Atoms
Solvent Atoms295
Heterogen Atoms70

Software

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