4Z35

Crystal Structure of Human Lysophosphatidic Acid Receptor 1 in complex with ONO-9910539


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1LIPIDIC CUBIC PHASE5.52930.1 M sodium citrate (pH 5.5), 34 - 38% (v/v) PEG400 and 200 mM ammonium acetate
Crystal Properties
Matthew coefficientSolvent content
2.9558.33

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 34.61α = 90
b = 112.4β = 90
c = 155.67γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2012-12-01MSINGLE WAVELENGTH
21x-ray100CCDMARMOSAIC 300 mm CCD2012-12-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-D1.033APS23-ID-D
2SYNCHROTRONAPS BEAMLINE 23-ID-B1.033APS23-ID-B

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
12.947780.1442.61162761.28
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)
12.93.1620.4911.7

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 REPLACEMENTTHROUGHOUTPDB ids 3V2Y and 4EIY2.9301162758481.90.26570.2650.2791RANDOM99.28
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]
4.3229-4.0348-0.2881
RMS Deviations
KeyRefinement Restraint Deviation
t_other_torsion2.64
t_omega_torsion1.63
t_angle_deg0.92
t_bond_d0.009
t_improper_torsion
t_pseud_angle
t_gen_planes
t_it
t_nbd
t_incorr_chiral_ct
RMS Deviations
KeyRefinement Restraint Deviation
t_other_torsion2.64
t_omega_torsion1.63
t_angle_deg0.92
t_bond_d0.009
t_improper_torsion
t_pseud_angle
t_gen_planes
t_it
t_nbd
t_incorr_chiral_ct
t_dihedral_angle_d
t_trig_c_planes
t_chiral_improper_torsion
t_sum_occupancies
t_utility_distance
t_utility_angle
t_utility_torsion
t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2977
Nucleic Acid Atoms
Solvent Atoms3
Heterogen Atoms59

Software

Software
Software NamePurpose
BUSTERrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing