3FMD

Crystal Structure of Human Haspin with an Isoquinoline ligand


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.527720% PEG 3350, 0.20M Na(malonate), pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
3.0860.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.51α = 90
b = 73.66β = 90
c = 87.74γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV2008-06-26MSINGLE 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
1229.24889.50.130.135.73.53460730973
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)
122.1181.80.4942.13.44971

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 REPLACEMENTTHROUGHOUTPDB ENTRY 2VUW2293460130757137888.890.2260.2260.2240.283RANDOM12.934
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]
0.350.09-0.44
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.342
r_dihedral_angle_3_deg13.616
r_dihedral_angle_4_deg13.557
r_dihedral_angle_1_deg6.578
r_mcangle_it3.631
r_mcbond_it2.709
r_angle_refined_deg1.581
r_angle_other_deg0.939
r_mcbond_other0.876
r_chiral_restr0.097
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.342
r_dihedral_angle_3_deg13.616
r_dihedral_angle_4_deg13.557
r_dihedral_angle_1_deg6.578
r_mcangle_it3.631
r_mcbond_it2.709
r_angle_refined_deg1.581
r_angle_other_deg0.939
r_mcbond_other0.876
r_chiral_restr0.097
r_bond_refined_d0.016
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
r_scbond_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2618
Nucleic Acid Atoms
Solvent Atoms381
Heterogen Atoms32

Software

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