8RUO | pdb_00008ruo

D44E mutant crystal structure of LpMIP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 8BJC 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.2298MES 50mM Magnesium chloride 500mM Zinc chloride 50mM PEG 8000 15%
Crystal Properties
Matthews coefficientSolvent content
3.4564.37

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.185α = 90
b = 77.185β = 90
c = 103.517γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER R 4M2024-01-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE MASSIF-30.9677ESRFMASSIF-3

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
12.5443.0299.920.9513.591082971.76
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)
12.542.6311000.78

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.5443.021032250899.930.253550.250470.26850.318510.3253RANDOM70.023
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]
0.130.13-0.27
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg18.257
r_long_range_B_other15.598
r_long_range_B_refined15.594
r_scangle_other10.232
r_mcangle_it8.516
r_mcangle_other8.514
r_dihedral_angle_1_deg7.431
r_scbond_it6.766
r_scbond_other6.762
r_mcbond_it5.822
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg18.257
r_long_range_B_other15.598
r_long_range_B_refined15.594
r_scangle_other10.232
r_mcangle_it8.516
r_mcangle_other8.514
r_dihedral_angle_1_deg7.431
r_scbond_it6.766
r_scbond_other6.762
r_mcbond_it5.822
r_mcbond_other5.814
r_dihedral_angle_2_deg5.361
r_angle_refined_deg1.787
r_angle_other_deg0.586
r_chiral_restr0.086
r_bond_refined_d0.007
r_gen_planes_refined0.006
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 Atoms1567
Nucleic Acid Atoms
Solvent Atoms37
Heterogen Atoms21

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata scaling
XDSdata reduction
MoRDaphasing