2V8D

Crystal structure of mutant E159A of beta-alanine synthase from Saccharomyces kluyveri


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1R43PDB ENTRY 1R43

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6293TRISODIUM CITRATE, DIOXANE, ACETONE, DTT, PH 6.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K
Crystal Properties
Matthews coefficientSolvent content
2.4550

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.117α = 90
b = 77.143β = 97.12
c = 108.228γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2006-05-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-4ESRFID14-4

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
12.350970.0811.93.243156248.8
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)
12.32.4880.4622.7

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1R432.345.2240838219596.60.2320.230.276RANDOM27.42
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]
3.82.99-2.61-0.45
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.168
r_dihedral_angle_4_deg18.353
r_dihedral_angle_3_deg16.715
r_dihedral_angle_1_deg5.698
r_scangle_it1.616
r_angle_refined_deg1.131
r_scbond_it1.066
r_mcangle_it0.63
r_mcbond_it0.368
r_nbtor_refined0.298
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.168
r_dihedral_angle_4_deg18.353
r_dihedral_angle_3_deg16.715
r_dihedral_angle_1_deg5.698
r_scangle_it1.616
r_angle_refined_deg1.131
r_scbond_it1.066
r_mcangle_it0.63
r_mcbond_it0.368
r_nbtor_refined0.298
r_xyhbond_nbd_refined0.291
r_nbd_refined0.198
r_symmetry_vdw_refined0.192
r_symmetry_hbond_refined0.099
r_chiral_restr0.078
r_bond_refined_d0.01
r_gen_planes_refined0.003
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6679
Nucleic Acid Atoms
Solvent Atoms58
Heterogen Atoms4

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing