2RC9

Crystal structure of the NR3A ligand binding core complex with ACPC at 1.96 Angstrom resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2RC7Pdb entry 2RC7

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.72930.2 M Mg Acetate, 0.1 M NaCitrate, 14% PEG 3350, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.3347.11

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.675α = 90
b = 103.552β = 95.04
c = 59.798γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2007-04-15MSINGLE 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
11.964097.90.0888.52.9432394323911
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)
11.962.0396.40.3620.02592.7

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 2RC71.9619.914012840128210697.850.159210.159210.156460.21114RANDOM14.799
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]
-0.010.040.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.757
r_dihedral_angle_4_deg17.032
r_dihedral_angle_3_deg13.966
r_dihedral_angle_1_deg6.089
r_scangle_it3.513
r_scbond_it2.241
r_angle_refined_deg1.45
r_mcangle_it1.383
r_mcbond_it0.861
r_nbtor_refined0.307
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.757
r_dihedral_angle_4_deg17.032
r_dihedral_angle_3_deg13.966
r_dihedral_angle_1_deg6.089
r_scangle_it3.513
r_scbond_it2.241
r_angle_refined_deg1.45
r_mcangle_it1.383
r_mcbond_it0.861
r_nbtor_refined0.307
r_symmetry_hbond_refined0.28
r_symmetry_vdw_refined0.211
r_nbd_refined0.209
r_xyhbond_nbd_refined0.154
r_chiral_restr0.102
r_bond_refined_d0.014
r_gen_planes_refined0.006
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 Atoms4524
Nucleic Acid Atoms
Solvent Atoms513
Heterogen Atoms14

Software

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