7VCE

Structural studies of human inositol monophosphatase-1 inhibition by ebselen


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4AS4 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP292.150.2 M magnesium formate and 20% (wt/vol) PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.2439.69

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.29α = 90
b = 75.72β = 95.6
c = 57.51γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152013-12-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.979DiamondI04

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
12.645.0498.750.9938.571.814825
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)
12.62.6930.733

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-VALUE4AS42.645.041482576498.780.230.20060.243637.693
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]
1.162-2.2990.626-1.312
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.411
r_dihedral_angle_3_deg15.181
r_dihedral_angle_4_deg12.867
r_dihedral_angle_1_deg5.012
r_lrange_it4.222
r_lrange_other4.168
r_mcangle_other2.78
r_mcangle_it2.763
r_scangle_other2.695
r_scangle_it2.684
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.411
r_dihedral_angle_3_deg15.181
r_dihedral_angle_4_deg12.867
r_dihedral_angle_1_deg5.012
r_lrange_it4.222
r_lrange_other4.168
r_mcangle_other2.78
r_mcangle_it2.763
r_scangle_other2.695
r_scangle_it2.684
r_angle_other_deg1.893
r_scbond_other1.743
r_mcbond_other1.714
r_scbond_it1.703
r_mcbond_it1.679
r_angle_refined_deg1.169
r_symmetry_xyhbond_nbd_refined0.379
r_xyhbond_nbd_refined0.294
r_nbd_other0.242
r_symmetry_nbd_other0.201
r_nbd_refined0.186
r_nbtor_refined0.178
r_symmetry_nbd_refined0.158
r_symmetry_nbtor_other0.092
r_symmetry_xyhbond_nbd_other0.073
r_chiral_restr0.06
r_bond_other_d0.055
r_dihedral_angle_other_3_deg0.034
r_bond_refined_d0.006
r_gen_planes_refined0.003
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3707
Nucleic Acid Atoms
Solvent Atoms128
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing