1O5K | pdb_00001o5k

Crystal structure of Dihydrodipicolinate synthase (TM1521) from Thermotoga maritima at 1.80 A resolution


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION,SITTING DROP,NANODROP7.529328% PEG-400, 0.1M Sodium HEPES pH 7.5, 0.2M Calcium chloride dihydrate, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.1241.42

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.672α = 90
b = 140.768β = 90
c = 155.943γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 4bent conical Si-mirror (Rh coating)2003-04-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 14-BM-CAPS14-BM-C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.61501000.09612.184.25686826868230.5
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.611.6765.470.7121.041.745042

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1DHP1.835.6149783265693.330.141740.139410.150.185930.19RANDOM25.358
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]
1.84-0.51-1.32
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.241
r_dihedral_angle_4_deg20.002
r_dihedral_angle_3_deg13.619
r_scangle_it7.692
r_dihedral_angle_1_deg6.139
r_scbond_it5.534
r_mcangle_it3.014
r_mcbond_it2.275
r_angle_refined_deg1.608
r_angle_other_deg0.857
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.241
r_dihedral_angle_4_deg20.002
r_dihedral_angle_3_deg13.619
r_scangle_it7.692
r_dihedral_angle_1_deg6.139
r_scbond_it5.534
r_mcangle_it3.014
r_mcbond_it2.275
r_angle_refined_deg1.608
r_angle_other_deg0.857
r_symmetry_vdw_other0.342
r_symmetry_hbond_refined0.248
r_symmetry_vdw_refined0.226
r_nbd_refined0.221
r_nbd_other0.184
r_xyhbond_nbd_refined0.158
r_chiral_restr0.099
r_nbtor_other0.087
r_bond_refined_d0.017
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4539
Nucleic Acid Atoms
Solvent Atoms508
Heterogen Atoms1

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement