3IQ7

Crystal Structure of human Haspin in complex with 5-Iodotubercidin


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2VUW 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52770.4M (NH4)H2PO4, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.957.53

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 69.034α = 90
b = 78.486β = 90
c = 87.048γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV2008-11-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E SUPERBRIGHT1.5

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
1229.151000.0850.08510.63.6326763267627.6
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.111000.620.6223.54697

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2VUW229.153263332620144099.960.1740.1740.1720.207RANDOM20.973
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]
0.670.24-0.9
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.625
r_dihedral_angle_4_deg14.328
r_dihedral_angle_3_deg12.73
r_scangle_it9.161
r_scbond_it7.856
r_dihedral_angle_1_deg6.197
r_mcangle_it4.755
r_mcbond_it3.5
r_angle_refined_deg1.554
r_angle_other_deg1.279
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.625
r_dihedral_angle_4_deg14.328
r_dihedral_angle_3_deg12.73
r_scangle_it9.161
r_scbond_it7.856
r_dihedral_angle_1_deg6.197
r_mcangle_it4.755
r_mcbond_it3.5
r_angle_refined_deg1.554
r_angle_other_deg1.279
r_mcbond_other1.217
r_chiral_restr0.098
r_bond_refined_d0.016
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2599
Nucleic Acid Atoms
Solvent Atoms262
Heterogen Atoms34

Software

Software
Software NamePurpose
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
MOSFLMdata reduction