2NM3

Crystal structure of dihydroneopterin aldolase from S. aureus in complex with (1S,2S)-monapterin at 1.68 angstrom resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1DHNPDB ENTRY 1DHN

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.52921.4M Sodium acetate, 0.2M Imidazole, 0.1M Sodium cacodylate, 10mM Tris-HCL, pH 6.50, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties
Matthews coefficientSolvent content
2.1241.87

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.191α = 90
b = 61.191β = 90
c = 124.528γ = 90
Symmetry
Space GroupI 4 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 4MIRROR2004-04-03MSINGLE 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
11.6830980.05831.3210.47213718
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)
11.681.7488.70.3882.099.31

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (All)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE RPDB ENTRY 1DHN1.683041292872092.90.2270.2240.262RANDOM
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]
Coordinate Error
Structure Solution MethodRefinement High ResolutionRefinement Low Resolution
31156.5
RMS Deviations
KeyRefinement Restraint Deviation
s_similar_adp_cmpnt0.087
s_anti_bump_dis_restr0.076
s_zero_chiral_vol0.054
s_non_zero_chiral_vol0.044
s_angle_d0.023
s_from_restr_planes0.023
s_bond_d0.007
s_similar_dist
s_rigid_bond_adp_cmpnt
s_approx_iso_adps
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms967
Nucleic Acid Atoms
Solvent Atoms172
Heterogen Atoms22

Software

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