2HMC

The Crystal Structure of Dihydrodipicolinate Synthase DapA from Agrobacterium tumefaciens


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.52950.2M Tri-Lithium Citrate, 20% PEG3350, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.3748.08

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 101.102α = 90
b = 101.102β = 90
c = 120.914γ = 120
Symmetry
Space GroupP 63 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDSBC-3mirrors2006-06-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-BM0.97910APS19-BM

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
11.931.9299.80.1046.125.62927529211
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)
11.91.9399.60.5553.518.61404

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONSADTHROUGHOUT1.931.922530125301281396.060.193150.193150.187150.24674RANDOM32.017
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]
1.670.831.67-2.5
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.235
r_dihedral_angle_4_deg18.209
r_dihedral_angle_3_deg14.975
r_dihedral_angle_1_deg5.815
r_scangle_it3.549
r_scbond_it2.305
r_angle_refined_deg1.415
r_mcangle_it1.252
r_mcbond_it0.899
r_nbtor_refined0.311
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.235
r_dihedral_angle_4_deg18.209
r_dihedral_angle_3_deg14.975
r_dihedral_angle_1_deg5.815
r_scangle_it3.549
r_scbond_it2.305
r_angle_refined_deg1.415
r_mcangle_it1.252
r_mcbond_it0.899
r_nbtor_refined0.311
r_nbd_refined0.214
r_symmetry_vdw_refined0.194
r_xyhbond_nbd_refined0.17
r_symmetry_hbond_refined0.149
r_chiral_restr0.099
r_bond_refined_d0.014
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2388
Nucleic Acid Atoms
Solvent Atoms409
Heterogen Atoms2

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
HKL-3000phasing
SHELXEmodel building
SOLVEphasing
RESOLVEphasing
ARP/wARPmodel building