2V8C

Mouse Profilin IIa in complex with the proline-rich domain of VASP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1D1JPDB ENTRY 1D1J

Crystallization

Crystal Properties
Matthews coefficientSolvent content
1.9736.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.73α = 90
b = 47.09β = 90
c = 68.58γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2003-06-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.1BESSY14.1

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
11.982099.80.0816.56.810355-326
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)
11.982.0299.50.3455.9

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 1D1J1.98201035551899.80.1460.1450.181RANDOM14.88
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]
-1.220.041.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.037
r_scangle_it3.792
r_mcangle_it2.515
r_scbond_it2.462
r_mcbond_it1.507
r_angle_refined_deg1.172
r_angle_other_deg0.785
r_symmetry_vdw_other0.256
r_nbd_other0.245
r_nbd_refined0.188
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.037
r_scangle_it3.792
r_mcangle_it2.515
r_scbond_it2.462
r_mcbond_it1.507
r_angle_refined_deg1.172
r_angle_other_deg0.785
r_symmetry_vdw_other0.256
r_nbd_other0.245
r_nbd_refined0.188
r_symmetry_hbond_refined0.141
r_xyhbond_nbd_refined0.133
r_nbtor_other0.081
r_chiral_restr0.071
r_symmetry_vdw_refined0.05
r_bond_refined_d0.008
r_bond_other_d0.006
r_gen_planes_refined0.004
r_gen_planes_other0.001
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
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_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 Atoms1123
Nucleic Acid Atoms
Solvent Atoms119
Heterogen Atoms30

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing