8HDG | pdb_00008hdg

Small peptide enhances the binding of nutline-3a to MdmX


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7C3Y 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.529120% v/v Tacsimate pH7.0, 0.1 M HEPES pH7.5, 2% v/v Polythylene glycol 200
Crystal Properties
Matthews coefficientSolvent content
2.0740.69

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.844α = 90
b = 47.879β = 90.053
c = 92.233γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 X 16M2020-01-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL02U10.9792SSRFBL02U1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
11.6847.8441000.0920.0940.019125.423.743877
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.681.7199.81.2561.2890.2870.8419.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)Mean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTNONE7C3Y1.7347.84443877230299.9520.2060.20450.220.2410.2526.721
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]
0.386-0.070.403-0.789
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg16.793
r_dihedral_angle_6_deg16.152
r_dihedral_angle_2_deg11.9
r_lrange_other8.499
r_lrange_it8.494
r_dihedral_angle_1_deg7.293
r_scangle_it6.07
r_scangle_other6.069
r_mcangle_it4.106
r_mcangle_other4.105
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3140
Nucleic Acid Atoms
Solvent Atoms111
Heterogen Atoms232

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
HKL-3000data collection
MOLREPphasing