7F6M

Crystal structure of APC complexed with a peptide inhibitor MAI-516


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2910.2M Ammonium sulfate 0.1M Tris pH 8.0, 25% w/v PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.2445.03

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 87.751α = 90
b = 82.337β = 94.69
c = 49.743γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray93PIXELDECTRIS PILATUS 6M2020-01-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL19U10.978SSRFBL19U1

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
12.459.9599.30.959.83713724
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)
12.42.440.944

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 REPLACEMENTTHROUGHOUT5IZ62.459.951300272198.930.21050.20780.2564RANDOM38.329
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]
-1.51-0.43-4.035.53
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.294
r_dihedral_angle_4_deg21.473
r_dihedral_angle_3_deg15.223
r_dihedral_angle_1_deg5.338
r_angle_refined_deg1.049
r_angle_other_deg0.886
r_chiral_restr0.057
r_bond_refined_d0.007
r_gen_planes_refined0.004
r_bond_other_d0.003
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.294
r_dihedral_angle_4_deg21.473
r_dihedral_angle_3_deg15.223
r_dihedral_angle_1_deg5.338
r_angle_refined_deg1.049
r_angle_other_deg0.886
r_chiral_restr0.057
r_bond_refined_d0.007
r_gen_planes_refined0.004
r_bond_other_d0.003
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2709
Nucleic Acid Atoms
Solvent Atoms97
Heterogen Atoms55

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-3000data collection
pointlessdata scaling
PHASERphasing