6QMM

Crystal structure of Synecochoccus Spermidine Synthase in complex with putrescine, spermidine and MTA


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4YUV 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP294.150.1 M MES pH 6.0, 45 % v/v Pentaerythritol propoxylate (5/4 PO/OH)
Crystal Properties
Matthews coefficientSolvent content
2.1643

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.64α = 90
b = 63.82β = 92.72
c = 73.5γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 4M2016-04-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE MASSIF-30.9677ESRFMASSIF-3

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)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
12.1848.17990.07210.0830.99716.184.227391
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.182.270.2260.2610.956

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 REPLACEMENTTHROUGHOUT4YUV2.1848.1726118137598.30.14410.14160.1911RANDOM17.36
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]
1.210.43-0.07-1.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.971
r_dihedral_angle_4_deg22.329
r_dihedral_angle_3_deg14.88
r_dihedral_angle_1_deg7.423
r_angle_other_deg2.618
r_angle_refined_deg2.489
r_mcangle_it2.093
r_mcbond_other1.263
r_mcbond_it1.262
r_chiral_restr0.127
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.971
r_dihedral_angle_4_deg22.329
r_dihedral_angle_3_deg14.88
r_dihedral_angle_1_deg7.423
r_angle_other_deg2.618
r_angle_refined_deg2.489
r_mcangle_it2.093
r_mcbond_other1.263
r_mcbond_it1.262
r_chiral_restr0.127
r_bond_other_d0.035
r_gen_planes_other0.032
r_bond_refined_d0.023
r_gen_planes_refined0.017
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4411
Nucleic Acid Atoms
Solvent Atoms256
Heterogen Atoms61

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing