8QVS

Crystal structure of Ompk36 GD at 3500 eV based on a combination of spherical harmonics and analytical absorption corrections


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6RCK 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.62930.1M Lithium sulfate, 0.1M sodium citrate pH 5.6 and 12% PEG4000
Crystal Properties
Matthews coefficientSolvent content
3.1961.41

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 232.078α = 90
b = 74.7β = 112.21
c = 91.35γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray80PIXELDECTRIS PILATUS 12M2021-05-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I233.54DiamondI23

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)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
12.34107.4398.860.99824.921160652
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.342.4240.878

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT2.34107.4357401326198.770.194730.192620.23277RANDOM39.852
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]
-0.280.15-2.481.97
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg13.427
r_long_range_B_refined8.084
r_long_range_B_other8.075
r_dihedral_angle_2_deg7.436
r_dihedral_angle_1_deg6.854
r_scangle_other6.632
r_mcangle_it4.751
r_mcangle_other4.751
r_scbond_it4.359
r_scbond_other4.352
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg13.427
r_long_range_B_refined8.084
r_long_range_B_other8.075
r_dihedral_angle_2_deg7.436
r_dihedral_angle_1_deg6.854
r_scangle_other6.632
r_mcangle_it4.751
r_mcangle_other4.751
r_scbond_it4.359
r_scbond_other4.352
r_mcbond_it3.372
r_mcbond_other3.372
r_angle_refined_deg1.45
r_angle_other_deg0.512
r_chiral_restr0.067
r_bond_refined_d0.007
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
r_dihedral_angle_4_deg
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 Atoms8119
Nucleic Acid Atoms
Solvent Atoms196
Heterogen Atoms10

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing