4D9B

Pyridoxamine 5' phosphate (PMP) bound form of Salmonella typhimurium D-Cysteine desulfhydrase obtained after co-crystallization with D-cycloserine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4D8TPDB ENTRY 4D8T

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.62981.5M Ammonium sulphate, 15% (v/v) ethylene glycol, 0.1M HEPES, 0.2% Benzamidine, 10mM D-Cycloserine, pH 8.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.2444.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 66.318α = 90
b = 164.926β = 118.97
c = 68.314γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDbent collimating mirror and torroid2010-04-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM14ESRFBM14

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
11.675096.90.05333.944143652
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)
11.671.7389.90.2713.68

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 4D8T1.6739.91136354719197.50.172310.170540.20593RANDOM22.025
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]
0.01-0.010.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.046
r_dihedral_angle_4_deg21.094
r_dihedral_angle_3_deg13.644
r_dihedral_angle_1_deg6.516
r_scangle_it5.132
r_scbond_it3.376
r_angle_refined_deg2.231
r_mcangle_it2.183
r_mcbond_it1.399
r_chiral_restr0.171
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.046
r_dihedral_angle_4_deg21.094
r_dihedral_angle_3_deg13.644
r_dihedral_angle_1_deg6.516
r_scangle_it5.132
r_scbond_it3.376
r_angle_refined_deg2.231
r_mcangle_it2.183
r_mcbond_it1.399
r_chiral_restr0.171
r_bond_refined_d0.028
r_gen_planes_refined0.013
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9685
Nucleic Acid Atoms
Solvent Atoms887
Heterogen Atoms115

Software

Software
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling