3IJF

Crystal structure of cytidine deaminase from Mycobacterium tuberculosis


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2FR5 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5293100 mM HEPES and 4.3 M NaCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.3547.59

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.705α = 90
b = 75.338β = 90
c = 55.116γ = 90
Symmetry
Space GroupC 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAC Science DIP-30002009-02-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONLNLS BEAMLINE D03B-MX11.437LNLSD03B-MX1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.9922.27970.0860.086102.320845937422

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2fr51.9918.249374862143396.990.192640.190170.24015RANDOM17.537
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]
0.01-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.68
r_dihedral_angle_3_deg20.873
r_dihedral_angle_4_deg17.69
r_dihedral_angle_1_deg5.942
r_scangle_it4.037
r_scbond_it2.855
r_angle_refined_deg2.161
r_mcangle_it1.658
r_mcbond_it0.974
r_nbtor_refined0.312
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.68
r_dihedral_angle_3_deg20.873
r_dihedral_angle_4_deg17.69
r_dihedral_angle_1_deg5.942
r_scangle_it4.037
r_scbond_it2.855
r_angle_refined_deg2.161
r_mcangle_it1.658
r_mcbond_it0.974
r_nbtor_refined0.312
r_nbd_refined0.25
r_symmetry_vdw_refined0.239
r_symmetry_hbond_refined0.21
r_chiral_restr0.191
r_xyhbond_nbd_refined0.171
r_bond_refined_d0.019
r_gen_planes_refined0.008
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 Atoms893
Nucleic Acid Atoms
Solvent Atoms89
Heterogen Atoms1

Software

Software
Software NamePurpose
HKL-3000data collection
AMoREphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling