4WML

Crystal structure of Saccharomyces cerevisiae OMP synthase in complex with PRP(CH2)P


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2PRY 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52950.1 M NaHEPES pH 7.5, 10 % Isopropanol, 20 % PEG 4000
Crystal Properties
Matthews coefficientSolvent content
2.4850.31

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.56α = 90
b = 61.56β = 90
c = 132.49γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2013-11-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX II BEAMLINE I911-31.000MAX III911-3

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.7333.1497.40.05828.6313.52680726807
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.731.771001.4510.8

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2PRY1.733125402133797.40.213350.211380.25017RANDOM37.806
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]
1.681.68-3.35
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.303
r_dihedral_angle_3_deg15.734
r_dihedral_angle_4_deg14.946
r_long_range_B_refined8.04
r_long_range_B_other8.013
r_scangle_other6.401
r_dihedral_angle_1_deg6.169
r_mcangle_it5.134
r_mcangle_other5.132
r_scbond_it4.275
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.303
r_dihedral_angle_3_deg15.734
r_dihedral_angle_4_deg14.946
r_long_range_B_refined8.04
r_long_range_B_other8.013
r_scangle_other6.401
r_dihedral_angle_1_deg6.169
r_mcangle_it5.134
r_mcangle_other5.132
r_scbond_it4.275
r_scbond_other4.25
r_mcbond_it3.586
r_mcbond_other3.583
r_angle_refined_deg1.984
r_angle_other_deg0.936
r_chiral_restr0.117
r_bond_refined_d0.019
r_gen_planes_refined0.01
r_bond_other_d0.001
r_gen_planes_other0.001
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1668
Nucleic Acid Atoms
Solvent Atoms139
Heterogen Atoms23

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
Cootmodel building
MOLREPphasing