2X6M | pdb_00002x6m

Structure of a single domain camelid antibody fragment in complex with a C-terminal peptide of alpha-synuclein


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1HCVPDB ENTRY 1HCV

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.525% PEG6000, 100 MM HEPES PH 7.5, 100 MM LICL
Crystal Properties
Matthews coefficientSolvent content
2.0138.84

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.17α = 90
b = 63.12β = 90
c = 62.87γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray173IMAGE PLATEMAR555 FLAT PANELMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X11EMBL/DESY, HAMBURGX11

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.623099.90.1223.314.31548218.126
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.621.7199.90.544.314.2

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1HCV1.6243.5614361110199.930.15960.156340.170.202580.21RANDOM17.91
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]
-0.47-0.190.66
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.154
r_dihedral_angle_4_deg24.031
r_dihedral_angle_3_deg12.931
r_dihedral_angle_1_deg7.031
r_scangle_it5.539
r_scbond_it3.561
r_mcangle_it2.481
r_angle_refined_deg1.693
r_mcbond_it1.531
r_chiral_restr0.147
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms993
Nucleic Acid Atoms
Solvent Atoms208
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing