3C9F

Crystal structure of 5'-nucleotidase from Candida albicans SC5314


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52943M Sodium formate, 8% PEG 400, 10% Glycerol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties
Matthews coefficientSolvent content
3.2462.04

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 103.946α = 90
b = 106.74β = 90
c = 150.656γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray77CCDMAR CCD 165 mm2008-02-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 31-ID0.9796APS31-ID

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
11.855099.10.0963.96.5142886-0.5
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)
11.851.9296.80.850.55.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONSADTHROUGHOUT1.920127304396299.390.187560.18640.22524RANDOM39.572
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]
0.46-0.960.5
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.293
r_dihedral_angle_4_deg16.7
r_dihedral_angle_3_deg15.093
r_scangle_it8.289
r_dihedral_angle_1_deg6.47
r_scbond_it6.018
r_mcangle_it5.258
r_mcbond_it3.561
r_angle_refined_deg1.342
r_nbtor_refined0.307
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.293
r_dihedral_angle_4_deg16.7
r_dihedral_angle_3_deg15.093
r_scangle_it8.289
r_dihedral_angle_1_deg6.47
r_scbond_it6.018
r_mcangle_it5.258
r_mcbond_it3.561
r_angle_refined_deg1.342
r_nbtor_refined0.307
r_xyhbond_nbd_refined0.188
r_symmetry_hbond_refined0.175
r_nbd_refined0.168
r_symmetry_vdw_refined0.141
r_chiral_restr0.096
r_metal_ion_refined0.082
r_bond_refined_d0.011
r_gen_planes_refined0.005
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_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 Atoms8787
Nucleic Acid Atoms
Solvent Atoms833
Heterogen Atoms12

Software

Software
Software NamePurpose
SHELXDphasing
REFMACrefinement
MAR345data collection
HKL-2000data reduction
HKL-2000data scaling