2RCB

Crystal structure of the NR3B ligand binding core complex with D-serine at 1.62 Angstrom resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.22930.1 M NaCitrate, 17% PEG 4000, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.1542.87

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.779α = 90
b = 83.521β = 90
c = 144.959γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2006-12-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID1.00000APS22-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
11.624099.90.05214.54.5716577165711
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)
11.621.6898.50.3443.964.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPdb entry 1PB71.6236.256530565305552598.930.194550.194550.191780.22754RANDOM18.293
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]
-0.080.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.148
r_dihedral_angle_4_deg16.604
r_dihedral_angle_3_deg11.714
r_dihedral_angle_1_deg4.907
r_scangle_it2.473
r_mcangle_it1.988
r_scbond_it1.745
r_angle_refined_deg1.544
r_mcbond_it1.404
r_symmetry_vdw_refined0.322
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.148
r_dihedral_angle_4_deg16.604
r_dihedral_angle_3_deg11.714
r_dihedral_angle_1_deg4.907
r_scangle_it2.473
r_mcangle_it1.988
r_scbond_it1.745
r_angle_refined_deg1.544
r_mcbond_it1.404
r_symmetry_vdw_refined0.322
r_nbtor_refined0.318
r_nbd_refined0.22
r_xyhbond_nbd_refined0.192
r_symmetry_hbond_refined0.163
r_chiral_restr0.108
r_bond_refined_d0.013
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4390
Nucleic Acid Atoms
Solvent Atoms475
Heterogen Atoms20

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing