2BWQ

Crystal Structure of the RIM2 C2A-domain at 1.4 angstrom Resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.5293RAT RIM2 C2A-DOMAIN (RESIDUES 722-859) DISSOLVED IN 20 MM MES (PH 6.0), 150 MM NACL AND 1 MM EDTA WAS CONCENTRATED TO 25 MG/ML AND CRYSTALLIZED IN 17.5% (W/V) PEG 4000, 0.2 M (NH4)2SO4, 0.1M SODIUM ACETATE (PH 4.5) AT 20 DEGREES C USING THE HANGING-DROP VAPOR-DIFFUSION METHOD. CRYSTALS APPEARED OVERNIGHT AND GREW TO A FINAL SIZE OF 0.05 X 0.05 X 0.1 MM WITHIN TWO DAYS. PRIOR TO DATA COLLECTION, CRYSTALS WERE TRANSFERRED INTO A SOLUTION OF 20% (W/V) PEG 4000, 0.15M NACL, 0.2 M (NH4)2SO4, 0.1M SODIUM ACETATE (PH 4.5) AND 15% (V/V) ETHYLENE GLYCOL, AND THEN FLASH-COOLED IN LIQUID PROPANE.
Crystal Properties
Matthews coefficientSolvent content
1.829.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 25.455α = 90
b = 44.807β = 103.86
c = 55.756γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDCUSTOM2004-08-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-IDAPS19-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
11.4120.9198.50.0252.9423283-3
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)
11.411.43820.185.22.8

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 ENTRY 1V271.412021884138399.20.1830.1810.213RANDOM17.71
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]
0.410.120.41-0.75
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.433
r_dihedral_angle_4_deg23.439
r_dihedral_angle_3_deg12.82
r_dihedral_angle_1_deg6.838
r_scangle_it4.907
r_scbond_it3.279
r_mcangle_it2.147
r_angle_refined_deg1.914
r_mcbond_it1.44
r_nbtor_refined0.321
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.433
r_dihedral_angle_4_deg23.439
r_dihedral_angle_3_deg12.82
r_dihedral_angle_1_deg6.838
r_scangle_it4.907
r_scbond_it3.279
r_mcangle_it2.147
r_angle_refined_deg1.914
r_mcbond_it1.44
r_nbtor_refined0.321
r_nbd_refined0.244
r_symmetry_vdw_refined0.216
r_symmetry_hbond_refined0.161
r_xyhbond_nbd_refined0.157
r_chiral_restr0.132
r_bond_refined_d0.019
r_gen_planes_refined0.011
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_mcangle_other
r_scbond_other
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 Atoms1041
Nucleic Acid Atoms
Solvent Atoms110
Heterogen Atoms10

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing