2PNT

Crystal structure of the PDZ domain of human GRASP (GRP1) in complex with the C-terminal peptide of the metabotropic glutamate receptor type 1


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.72981.26M NaH2PO4, 0.14M K2HPO4, pH 7.7, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.7955.84

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 72.288α = 90
b = 72.288β = 90
c = 163.311γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2007-04-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA1.035SLSX10SA

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
12.14862.6221000.0918.81454614546
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.1482.2399.96.51411

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 entries 1GQ4, 2OCS2.14862.62137581375872999.910.209950.209950.208760.23198RANDOM34.719
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]
0.330.170.33-0.5
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.899
r_dihedral_angle_4_deg23.675
r_dihedral_angle_3_deg15.342
r_dihedral_angle_1_deg7.072
r_scangle_it3.934
r_scbond_it2.54
r_mcangle_it1.612
r_angle_refined_deg1.517
r_angle_other_deg0.923
r_mcbond_it0.919
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.899
r_dihedral_angle_4_deg23.675
r_dihedral_angle_3_deg15.342
r_dihedral_angle_1_deg7.072
r_scangle_it3.934
r_scbond_it2.54
r_mcangle_it1.612
r_angle_refined_deg1.517
r_angle_other_deg0.923
r_mcbond_it0.919
r_symmetry_vdw_refined0.257
r_symmetry_vdw_other0.255
r_symmetry_hbond_refined0.226
r_mcbond_other0.201
r_nbd_other0.198
r_nbd_refined0.197
r_nbtor_refined0.186
r_xyhbond_nbd_refined0.136
r_chiral_restr0.097
r_nbtor_other0.089
r_bond_refined_d0.016
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1414
Nucleic Acid Atoms
Solvent Atoms76
Heterogen Atoms1

Software

Software
Software NamePurpose
REFMACrefinement
MAR345data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing