4RW0

Crystal structure of a member of the lipolytic protein G-D-S-L family from Veillonella parvula DSM 2008


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72931.0 M K/Na tartrate, 0.2M Li2SO4, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
4.2771.21

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 121.65α = 90
b = 121.65β = 90
c = 84.173γ = 120
Symmetry
Space GroupP 63

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rmirrors2014-09-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.9794APS19-ID

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
123699.60.083195.9476704738922
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.03100

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Cut-off Sigma (I)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSADTHROUGHOUT236224698544601238498.340.160.158810.157350.18628RANDOM31.767
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]
0.140.140.14-0.45
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.418
r_dihedral_angle_4_deg20.903
r_dihedral_angle_3_deg14.153
r_dihedral_angle_1_deg5.69
r_angle_refined_deg1.759
r_angle_other_deg0.873
r_chiral_restr0.124
r_bond_refined_d0.021
r_gen_planes_refined0.009
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.418
r_dihedral_angle_4_deg20.903
r_dihedral_angle_3_deg14.153
r_dihedral_angle_1_deg5.69
r_angle_refined_deg1.759
r_angle_other_deg0.873
r_chiral_restr0.124
r_bond_refined_d0.021
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2882
Nucleic Acid Atoms
Solvent Atoms343
Heterogen Atoms14

Software

Software
Software NamePurpose
SBC-Collectdata collection
HKL-3000phasing
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling