3DRH

Crystal structure of Lactococcal OppA co-crystallized with Leu-enkephalin in an open conformation


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3DRF 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP72930.2M NaCl, 0.1M Na-Hepes, 20% PEG 6000, pH 7.0, vapor diffusion, hanging drop, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.1643.05

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 39.707α = 90
b = 123.007β = 102.1
c = 59.308γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC Q2102007-07-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-10.934ESRFID14-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.741.0387.10.0540.05410.81.660984
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.71.79890.3650.36521.615707

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 REPLACEMENTTHROUGHOUT3DRF1.74160836310399.670.1670.1650.205RANDOM10.592
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]
-0.27-0.06-0.350.6
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.413
r_dihedral_angle_4_deg22.253
r_dihedral_angle_3_deg12.951
r_dihedral_angle_1_deg6.507
r_scangle_it3.238
r_scbond_it2.087
r_angle_refined_deg1.339
r_mcangle_it1.285
r_angle_other_deg0.882
r_mcbond_it0.726
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.413
r_dihedral_angle_4_deg22.253
r_dihedral_angle_3_deg12.951
r_dihedral_angle_1_deg6.507
r_scangle_it3.238
r_scbond_it2.087
r_angle_refined_deg1.339
r_mcangle_it1.285
r_angle_other_deg0.882
r_mcbond_it0.726
r_mcbond_other0.195
r_chiral_restr0.08
r_bond_refined_d0.013
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4383
Nucleic Acid Atoms
Solvent Atoms746
Heterogen Atoms

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction