7NZC

First SH3 domain of POSH (Plenty of SH3 Domains protein)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2SRCmodified 2SRC

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION82930.2 M NaF, 22% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.447.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 35.962α = 90
b = 35.962β = 90
c = 181.333γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 XE 16MMonochromators2019-08-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.9795DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)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
11.1130.7960.99926.119.42677
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.111.130.5651.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUEmodified 2SRC1.11130.69426656132192.5780.1480.14680.177517.845
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]
0.0430.0220.043-0.141
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.772
r_dihedral_angle_4_deg31.468
r_mcangle_it26.534
r_mcangle_other26.493
r_lrange_it26.469
r_lrange_other26.451
r_scangle_it24.836
r_scangle_other24.809
r_scbond_it18.746
r_scbond_other18.745
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.772
r_dihedral_angle_4_deg31.468
r_mcangle_it26.534
r_mcangle_other26.493
r_lrange_it26.469
r_lrange_other26.451
r_scangle_it24.836
r_scangle_other24.809
r_scbond_it18.746
r_scbond_other18.745
r_mcbond_other16.45
r_mcbond_it16.418
r_dihedral_angle_3_deg11.326
r_dihedral_angle_1_deg7.622
r_rigid_bond_restr3.128
r_angle_refined_deg1.677
r_angle_other_deg1.388
r_symmetry_xyhbond_nbd_refined0.253
r_nbd_refined0.208
r_symmetry_nbd_other0.183
r_xyhbond_nbd_refined0.181
r_nbtor_refined0.179
r_symmetry_nbd_refined0.17
r_nbd_other0.155
r_symmetry_nbtor_other0.087
r_chiral_restr0.081
r_bond_refined_d0.01
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms502
Nucleic Acid Atoms
Solvent Atoms138
Heterogen Atoms15

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
PHASERphasing