3WJZ

Orotidine 5'-monophosphate decarboxylase D75N mutant from M. thermoautotrophicus complexed with 6-amino-UMP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3WJY 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION9293Sodium citrate, pH 9, VAPOR DIFFUSION, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.0239.24

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.067α = 90
b = 103.595β = 90
c = 73.705γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 14-BM-C0.9000APS14-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
11.3951.781000.04839.845280
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)
11.391.411000.307

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 SYNTHESISTHROUGHOUT3WJY1.395045007225999.950.15790.1570.17447RANDOM17.4857
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]
0.15-0.490.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.735
r_dihedral_angle_4_deg19.338
r_dihedral_angle_3_deg12.172
r_dihedral_angle_1_deg5.533
r_scangle_it4.338
r_scbond_it2.593
r_mcangle_it1.443
r_angle_refined_deg1.442
r_mcbond_it0.796
r_chiral_restr0.089
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.735
r_dihedral_angle_4_deg19.338
r_dihedral_angle_3_deg12.172
r_dihedral_angle_1_deg5.533
r_scangle_it4.338
r_scbond_it2.593
r_mcangle_it1.443
r_angle_refined_deg1.442
r_mcbond_it0.796
r_chiral_restr0.089
r_bond_refined_d0.011
r_gen_planes_refined0.01
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1630
Nucleic Acid Atoms
Solvent Atoms174
Heterogen Atoms35

Software

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