2Y6N

STRUCTURE OF LINEAR GRAMICIDIN D OBTAINED USING TYPE I CRYSTALS GROWN IN A 8.8 MONOACYLGLYCEROL LIPID CUBIC PHASE.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2Y5MPDB ENTRY 2Y5M

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1LIPIDIC CUBIC PHASE30 %(W/V) POLYETHYLENE GLYCOL (PEG) 8000, 0.2 M NH4SO4, LIPIDIC CUBIC PHASE OF 8.8 MAG (SN-1-O-(CIS-8)HEXADECENYLGLYCEROL) WAS USED IN A RATIO OF 1:20 (MOL/MOL) GRAMICIDIN D TO 8.8 MAG.
Crystal Properties
Matthews coefficientSolvent content
2.652

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 30.616α = 90
b = 62.783β = 100.02
c = 30.602γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH MX-300SI(111) DOUBLE CRYSTAL2009-02-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-BAPS23-ID-B

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
11.2630.1596.40.0622.67.12832029.7
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)
11.261.2976.90.283.53.2

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 2Y5M1.2630.1528320153696.430.149170.148030.140.169830.16RANDOM11.441
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]
-0.91-0.51.77-1.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.604
r_sphericity_free18.263
r_sphericity_bonded12.4
r_dihedral_angle_3_deg8.763
r_scangle_it7.775
r_scbond_it6.05
r_mcangle_it4.55
r_dihedral_angle_1_deg4.523
r_rigid_bond_restr3.804
r_mcbond_it3.133
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms816
Nucleic Acid Atoms
Solvent Atoms2
Heterogen Atoms98

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing