3ZR1 | pdb_00003zr1

Crystal structure of human MTH1


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3FK9PDB ENTRY 3FK9

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
126 % PEG6000, 0.1 M SODIUM ACETATE TRIHYDRATE PH 4.0, 0.2 M LI2SO4
Crystal Properties
Matthews coefficientSolvent content
2.2846

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.52α = 90
b = 67.08β = 90
c = 80.13γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2011-03-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.1BESSY14.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.93499.20.111.65.125933
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)
11.9297.80.573.35

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 3FK91.951.4424313131198.810.193390.190670.20.244550.25RANDOM18.576
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]
-1.31-0.431.74
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.742
r_dihedral_angle_3_deg13.607
r_dihedral_angle_4_deg10.401
r_dihedral_angle_1_deg7.1
r_scangle_it5.459
r_scbond_it3.371
r_mcangle_it1.92
r_angle_refined_deg1.831
r_angle_other_deg1.279
r_mcbond_it1.038
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.742
r_dihedral_angle_3_deg13.607
r_dihedral_angle_4_deg10.401
r_dihedral_angle_1_deg7.1
r_scangle_it5.459
r_scbond_it3.371
r_mcangle_it1.92
r_angle_refined_deg1.831
r_angle_other_deg1.279
r_mcbond_it1.038
r_mcbond_other0.227
r_chiral_restr0.121
r_bond_refined_d0.022
r_gen_planes_refined0.009
r_gen_planes_other0.003
r_bond_other_d0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2476
Nucleic Acid Atoms
Solvent Atoms176
Heterogen Atoms28

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
BALBESphasing