5UV6

Crystal structure of human Opioid Binding Protein/Cell Adhesion Molecule Like (OPCML)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5293A 50/50 (v/v) mix of 1.6 M MgSO4, 0.1 M MES pH 6.5 with 20% PEG 8000, 100 mM HEPES pH 7.5.
Crystal Properties
Matthews coefficientSolvent content
4.6673.62

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 93.564α = 90
b = 93.564β = 90
c = 262.158γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2016-02-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 31-ID0.97931APS31-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
12.6518.595.810.170.0470.9969.7114.43466562.8618429607
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.652.74488.82.740.740.6851.214.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONSIRASFREE R-VALUE2.6500197760818.44270156541.326933253533372171396.20063418850.2849497001670.2840831411820.30028012510284.6421742087
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d11.4187860743
f_angle_d0.881733671118
f_chiral_restr0.0538547637936
f_bond_d0.00581078481975
f_plane_restr0.00472003162303
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4176
Nucleic Acid Atoms
Solvent Atoms40
Heterogen Atoms134

Software

Software
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHENIXphasing