5Z9O

The crystal structure of Cyclopropane-fatty-acyl-phospholipid synthase from Lactobacillus acidophilus


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1L1E 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2921.5 M ammonium sulfate, 0.1 M potassium sodium tartrate tetrahydrate, 0.1 M sodium citrate tribasic dehydrate
Crystal Properties
Matthews coefficientSolvent content
3.7567.22

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 120.982α = 90
b = 120.982β = 90
c = 163.487γ = 120
Symmetry
Space GroupP 61

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDNonius Kappa CCD2017-12-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL18U11.0SSRFBL18U1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.788.2199.945.24.337057
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.7032.773

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 REPLACEMENTTHROUGHOUT1L1E2.744.10635208185299.920.176960.175150.21258RANDOM49.138
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]
0.040.020.04-0.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41
r_long_range_B_refined34.754
r_dihedral_angle_3_deg19.984
r_dihedral_angle_4_deg18.749
r_dihedral_angle_1_deg6.768
r_mcangle_it5.872
r_scbond_it4.737
r_mcbond_it3.726
r_angle_refined_deg1.814
r_chiral_restr0.125
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41
r_long_range_B_refined34.754
r_dihedral_angle_3_deg19.984
r_dihedral_angle_4_deg18.749
r_dihedral_angle_1_deg6.768
r_mcangle_it5.872
r_scbond_it4.737
r_mcbond_it3.726
r_angle_refined_deg1.814
r_chiral_restr0.125
r_bond_refined_d0.013
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_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_it
r_scangle_other
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 Atoms6012
Nucleic Acid Atoms
Solvent Atoms262
Heterogen Atoms102

Software

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