1S5W

Crystal Structure Analysis of a mutant of DIHYDRODIPICOLINATE SYNTHASE--residue Tyr133 to Phe133


X-RAY DIFFRACTION

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
3.6566.06

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 121.206α = 90
b = 121.206β = 90
c = 110.784γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110IMAGE PLATEMARRESEARCH2002-11-20MSINGLE 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
12.325099.70.09440716
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)
2.322.3899.60.318

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 REPLACEMENTTHROUGHOUT1DHP2.3220.163865120381000.179680.179680.178070.21093RANDOM27.065
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]
-0.25-0.12-0.250.37
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.211
r_scangle_it2.678
r_scbond_it1.504
r_angle_refined_deg1.318
r_mcangle_it0.914
r_angle_other_deg0.857
r_mcbond_it0.467
r_nbd_other0.235
r_symmetry_vdw_refined0.219
r_symmetry_vdw_other0.209
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.211
r_scangle_it2.678
r_scbond_it1.504
r_angle_refined_deg1.318
r_mcangle_it0.914
r_angle_other_deg0.857
r_mcbond_it0.467
r_nbd_other0.235
r_symmetry_vdw_refined0.219
r_symmetry_vdw_other0.209
r_nbd_refined0.199
r_xyhbond_nbd_refined0.14
r_symmetry_hbond_refined0.128
r_nbtor_other0.124
r_chiral_restr0.076
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 Atoms4321
Nucleic Acid Atoms
Solvent Atoms273
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling