5FAR

Crystal structure of dihydroneopterin aldolase from Bacillus anthracis complex with 9-METHYLGUANINE


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2NM2 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2970.2 M Ammonium acetate, 0.1M Bis-Tris, 25% PEG3350
Crystal Properties
Matthews coefficientSolvent content
2.5251.22

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.795α = 90
b = 138.209β = 89.97
c = 63.933γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2015-07-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.97934APS19-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
1245.2184.70.1110.1240.0557.54.662246
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.0367.10.5850.6620.3030.763.92443

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2NM2245.1759338302483.50.194940.193120.23253RANDOM47.535
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]
-40.64-5.0589.11-48.48
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.005
r_dihedral_angle_3_deg16.105
r_dihedral_angle_4_deg14.111
r_dihedral_angle_1_deg7.379
r_long_range_B_refined5.057
r_long_range_B_other5.042
r_angle_refined_deg1.468
r_mcangle_it1.296
r_mcangle_other1.296
r_scangle_other0.945
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.005
r_dihedral_angle_3_deg16.105
r_dihedral_angle_4_deg14.111
r_dihedral_angle_1_deg7.379
r_long_range_B_refined5.057
r_long_range_B_other5.042
r_angle_refined_deg1.468
r_mcangle_it1.296
r_mcangle_other1.296
r_scangle_other0.945
r_angle_other_deg0.93
r_mcbond_it0.728
r_mcbond_other0.728
r_scbond_it0.586
r_scbond_other0.586
r_chiral_restr0.083
r_bond_refined_d0.01
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7831
Nucleic Acid Atoms
Solvent Atoms137
Heterogen Atoms96

Software

Software
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-3000data reduction
MOLREPphasing
BUCCANEERmodel building
Cootmodel building