1S5T

Crystal Structure Analysis of a mutant of DIHYDRODIPICOLINATE SYNTHASE--residue thr44 to val44


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP10277Drop contains: potassium phosphate (0.0012ml, 1.8M, pH10), N-octyl-beta-R-glucopyrandoside (0.0006ml, 6% w/v), VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
3.6265.72

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 121.059α = 90
b = 121.059β = 90
c = 110.882γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110IMAGE PLATEMARRESEARCH2002-11-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.5418

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
12.35094.30.09339811
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)
2.32.3887.70.32

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1DHP2.320.993772019941000.179660.179660.177880.21343RANDOM25.302
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]
-0.35-0.17-0.350.52
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.22
r_scangle_it2.467
r_scbond_it1.419
r_angle_refined_deg1.38
r_angle_other_deg0.893
r_mcangle_it0.884
r_mcbond_it0.459
r_nbd_other0.239
r_symmetry_vdw_other0.208
r_nbd_refined0.199
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.22
r_scangle_it2.467
r_scbond_it1.419
r_angle_refined_deg1.38
r_angle_other_deg0.893
r_mcangle_it0.884
r_mcbond_it0.459
r_nbd_other0.239
r_symmetry_vdw_other0.208
r_nbd_refined0.199
r_nbtor_other0.153
r_symmetry_vdw_refined0.148
r_xyhbond_nbd_refined0.14
r_symmetry_hbond_refined0.14
r_chiral_restr0.079
r_bond_refined_d0.011
r_gen_planes_other0.006
r_gen_planes_refined0.005
r_bond_other_d0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4312
Nucleic Acid Atoms
Solvent Atoms321
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling