2NM2

Crystal structure of dihydroneopterin aldolase from S. aureus in complex with (1S,2R)-neopterin at 1.50 Angstrom resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2NM3PDB ENTRY 2NM3

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.52920.8M Sodium-potassium tartrate, 0.1M HEPES, 10mM Tris-HCL, pH 7.50, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties
Matthews coefficientSolvent content
2.0138.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.033α = 90
b = 60.033β = 90
c = 123.057γ = 90
Symmetry
Space GroupP 42

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 4MIRROR2003-08-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X9BNSLSX9B

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
11.73092.10.05318.53.84391518.2
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)
11.71.7688.30.3591.982.2

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 REPLACEMENTTHROUGHOUTPDB ENTRY 2NM31.722.46420552047880.220.220.262RANDOM26.8
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]
1.091.09-2.18
Coordinate Error
Structure Solution MethodRefinement High ResolutionRefinement Low Resolution
4685
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d23.9
c_scangle_it3.95
c_scbond_it2.64
c_mcangle_it2.14
c_angle_deg1.4
c_mcbond_it1.4
c_improper_angle_d0.76
c_bond_d0.007
c_bond_d_na
c_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d23.9
c_scangle_it3.95
c_scbond_it2.64
c_mcangle_it2.14
c_angle_deg1.4
c_mcbond_it1.4
c_improper_angle_d0.76
c_bond_d0.007
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3868
Nucleic Acid Atoms
Solvent Atoms642
Heterogen Atoms72

Software

Software
Software NamePurpose
CNSrefinement
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing