5G4J

Phospholyase A1RDF1 from Arthrobacter in complex with phosphoethanolamine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5G4IPDB ENTRY 5G4I

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1624% (W/V) PEG 3350, 0.2 M (NH4)2SO4 AND 3% (V/V) 2-METHYL-2,4-PENTANEDIOL IN 0.1 M BIS-TRIS PROPANE BUFFER AT PH 6.0
Crystal Properties
Matthews coefficientSolvent content
2.3347

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 76.166α = 90
b = 96.371β = 90
c = 121.897γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray120PIXELDECTRIS PILATUS 6M2016-04-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I02DiamondI02

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
11.8764.5999.80.0814.56.5746892
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)
11.871.9599.90.672.66.8

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 5G4I1.8775.670978363699.770.168840.167310.20.199430.23RANDOM25.913
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]
-1.840.511.32
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.885
r_dihedral_angle_4_deg18.596
r_dihedral_angle_3_deg14.118
r_dihedral_angle_1_deg6.287
r_scbond_it3.127
r_mcangle_it3.081
r_mcbond_it2.382
r_mcbond_other2.381
r_angle_refined_deg1.915
r_angle_other_deg1.478
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6300
Nucleic Acid Atoms
Solvent Atoms476
Heterogen Atoms49

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing