3CVF

Crystal Structure of the carboxy terminus of Homer3


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1hanging drop7.62970.1 M Tris, 4.2 M NaCl, 10% glycerol, pH 7.6, hanging drop, temperature 297K
Crystal Properties
Matthews coefficientSolvent content
7.8384.29

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 172.029α = 90
b = 172.029β = 90
c = 66.446γ = 120
Symmetry
Space GroupP 65

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDQuantum-4 ADSC2006-11-09SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X26C0.9795NSLSX26C

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
12.95099.40.07814.57.225036
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)
2.9398.10.2555.6

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 REPLACEMENTTHROUGHOUT3CVE2.919.7323703126999.460.253910.25220.28698RANDOM57.781
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]
0.020.010.02-0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.723
r_dihedral_angle_3_deg24.372
r_dihedral_angle_4_deg21.713
r_dihedral_angle_1_deg8.105
r_scangle_it5.682
r_mcangle_it3.345
r_scbond_it3.326
r_mcbond_it2.603
r_angle_refined_deg2.312
r_symmetry_vdw_refined0.352
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.723
r_dihedral_angle_3_deg24.372
r_dihedral_angle_4_deg21.713
r_dihedral_angle_1_deg8.105
r_scangle_it5.682
r_mcangle_it3.345
r_scbond_it3.326
r_mcbond_it2.603
r_angle_refined_deg2.312
r_symmetry_vdw_refined0.352
r_nbtor_refined0.317
r_nbd_refined0.296
r_symmetry_hbond_refined0.287
r_xyhbond_nbd_refined0.187
r_chiral_restr0.167
r_bond_refined_d0.025
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 Atoms2288
Nucleic Acid Atoms
Solvent Atoms18
Heterogen Atoms

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
PHASERphasing