1Z9W

Tetrameric structure of apo-7,8-Dihydroneopterin Aldolase from Mycobacterium tuberculosis


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1NBUPDB ENTRY 1NBU

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.6300PEG 4000, SODIUM ACETATE, PH 4.6, pH 7.60, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Crystal Properties
Matthews coefficientSolvent content
1.7329

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 72.957α = 90
b = 72.957β = 90
c = 42.868γ = 90
Symmetry
Space GroupI 4

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42003-04-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X8C0.9786NSLSX8C

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
12.5100990.07831.339901
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)
12.531000.3717.6

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1NBU2.551.573548354839398.750.184410.184410.178540.23429RANDOM37.451
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]
-0.93-0.931.86
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.585
r_dihedral_angle_4_deg24.087
r_dihedral_angle_3_deg16.679
r_dihedral_angle_1_deg8.864
r_scangle_it5.585
r_scbond_it3.565
r_mcangle_it2.475
r_angle_refined_deg2.261
r_mcbond_it1.363
r_nbtor_refined0.315
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.585
r_dihedral_angle_4_deg24.087
r_dihedral_angle_3_deg16.679
r_dihedral_angle_1_deg8.864
r_scangle_it5.585
r_scbond_it3.565
r_mcangle_it2.475
r_angle_refined_deg2.261
r_mcbond_it1.363
r_nbtor_refined0.315
r_nbd_refined0.241
r_symmetry_vdw_refined0.24
r_xyhbond_nbd_refined0.194
r_chiral_restr0.139
r_symmetry_hbond_refined0.13
r_bond_refined_d0.018
r_gen_planes_refined0.01
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms821
Nucleic Acid Atoms
Solvent Atoms25
Heterogen Atoms

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
REFMACrefinement