3FLU

Crystal structure of dihydrodipicolinate synthase from the pathogen Neisseria meningitidis


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1YXC 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.32911.8M ammonium sulfate, 100mM Bis-Tris.HCl, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.4449.66

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.667α = 90
b = 115.684β = 90
c = 132.122γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152008-10-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I020.9796DiamondI02

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
11.999115.68499.90.0965.7843358425121.23
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)
122.071000.3495.78359

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 REPLACEMENTTHROUGHOUT1YXC2115.478432484214420199.870.1510.1480.191RANDOM20.562
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]
0.34-0.70.36
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.065
r_dihedral_angle_4_deg16.803
r_dihedral_angle_3_deg12.642
r_dihedral_angle_1_deg6.825
r_scangle_it6.212
r_scbond_it4.421
r_mcangle_it2.259
r_mcbond_it1.726
r_angle_refined_deg1.133
r_nbtor_refined0.309
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.065
r_dihedral_angle_4_deg16.803
r_dihedral_angle_3_deg12.642
r_dihedral_angle_1_deg6.825
r_scangle_it6.212
r_scbond_it4.421
r_mcangle_it2.259
r_mcbond_it1.726
r_angle_refined_deg1.133
r_nbtor_refined0.309
r_symmetry_vdw_refined0.242
r_nbd_refined0.213
r_symmetry_hbond_refined0.179
r_xyhbond_nbd_refined0.137
r_chiral_restr0.09
r_gen_planes_refined0.012
r_bond_refined_d0.01
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8722
Nucleic Acid Atoms
Solvent Atoms938
Heterogen Atoms264

Software

Software
Software NamePurpose
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
DNAdata collection
DENZOdata reduction
SCALEPACKdata scaling