6XY7

Human SHIP1 with magnesium and phosphate bound to the active site


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5OKM 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.529330 mM sodium nitrate, 30 mM dibasic sodium phosphate, 30 mM ammonium sulphate, 100 mM MES/imidazole, pH 6.5, 20 % PEG 500 MME, 10% PEG 20,000
Crystal Properties
Matthews coefficientSolvent content
2.0941.03

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.5α = 90
b = 79.088β = 90
c = 89.255γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 XE 16M2019-08-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.8266DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
11.08659.19387.60.1520.1550.030.99811.726.9159826
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.0931.1459.62.192.2460.480.6011.420.7

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-VALUE5OKM1.08659.193159810177585.9050.1360.13580.158714.339
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]
0.079-0.008-0.071
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.754
r_dihedral_angle_4_deg25.458
r_dihedral_angle_3_deg12.711
r_dihedral_angle_1_deg7.442
r_lrange_it3.416
r_lrange_other3.283
r_scangle_it2.709
r_scangle_other2.708
r_mcangle_other2.483
r_mcangle_it2.481
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.754
r_dihedral_angle_4_deg25.458
r_dihedral_angle_3_deg12.711
r_dihedral_angle_1_deg7.442
r_lrange_it3.416
r_lrange_other3.283
r_scangle_it2.709
r_scangle_other2.708
r_mcangle_other2.483
r_mcangle_it2.481
r_scbond_it2.127
r_scbond_other2.127
r_rigid_bond_restr1.901
r_mcbond_it1.889
r_mcbond_other1.881
r_angle_refined_deg1.702
r_angle_other_deg1.465
r_symmetry_nbd_refined0.223
r_nbd_other0.222
r_nbd_refined0.213
r_symmetry_nbd_other0.188
r_nbtor_refined0.171
r_symmetry_xyhbond_nbd_refined0.165
r_xyhbond_nbd_refined0.16
r_chiral_restr0.091
r_symmetry_nbtor_other0.086
r_bond_refined_d0.011
r_gen_planes_refined0.009
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3704
Nucleic Acid Atoms
Solvent Atoms489
Heterogen Atoms28

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
STARANISOdata scaling
PHASERphasing