3ZQ8

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2XDCPDB ENTRY 2XDC

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1LIPIDIC CUBIC PHASE8.51M LITHIUM SULFATE, 10 MM NICKEL CHLORIDE, 0.1 M TRIS HCL, PH 8.5, LIPIDIC CUBIC PHASE OF MONOVACCENIN (11.7 MAG)
Crystal Properties
Matthews coefficientSolvent content
2.340.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 23.96α = 90
b = 41.981β = 107.25
c = 32.429γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rTOROIDAL MIRROR2009-10-04MSINGLE 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
11.722.996.90.05234.76612215.8
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)
11.71.7578.90.2553.9

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 2XDC1.722.88630630696.890.168230.166220.21118RANDOM17.281
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]
0.02-0.03-0.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.113
r_dihedral_angle_3_deg13.357
r_dihedral_angle_1_deg5.934
r_scangle_it5.062
r_scbond_it3.48
r_mcangle_it2.6
r_angle_refined_deg1.828
r_mcbond_it1.646
r_chiral_restr0.158
r_bond_refined_d0.019
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.113
r_dihedral_angle_3_deg13.357
r_dihedral_angle_1_deg5.934
r_scangle_it5.062
r_scbond_it3.48
r_mcangle_it2.6
r_angle_refined_deg1.828
r_mcbond_it1.646
r_chiral_restr0.158
r_bond_refined_d0.019
r_gen_planes_refined0.017
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
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 Atoms544
Nucleic Acid Atoms
Solvent Atoms2
Heterogen Atoms44

Software

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