2J4E

THE ITP COMPLEX OF HUMAN INOSINE TRIPHOSPHATASE


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2CARPDB ENTRY 2CAR

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
10.2 M POTASSIUM CHLORIDE, 31 % (W/V) PEG 3350, AND THE PROTEIN WAS ADDED FROM A 50 MG/ML STOCK SOLUTION CONTAINING 10MM ITP AND 20 MM HEPES PH 7.5.
Crystal Properties
Matthews coefficientSolvent content
3.0158.81

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.998α = 85.12
b = 75.292β = 77.72
c = 110.793γ = 69.19
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMSINGLE 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
12.82097.60.117.9245773
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)
12.82.9597.40.421.82

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2CAR2.819.8145773246197.80.2040.2010.265RANDOM25.25
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]
-0.010.040.03-0.040.010.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.968
r_dihedral_angle_3_deg17.042
r_dihedral_angle_4_deg16.635
r_dihedral_angle_1_deg6.27
r_scangle_it1.191
r_angle_refined_deg1.184
r_angle_other_deg0.824
r_scbond_it0.751
r_mcangle_it0.514
r_mcbond_it0.403
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.968
r_dihedral_angle_3_deg17.042
r_dihedral_angle_4_deg16.635
r_dihedral_angle_1_deg6.27
r_scangle_it1.191
r_angle_refined_deg1.184
r_angle_other_deg0.824
r_scbond_it0.751
r_mcangle_it0.514
r_mcbond_it0.403
r_nbd_refined0.201
r_symmetry_vdw_other0.19
r_nbd_other0.185
r_nbtor_refined0.177
r_symmetry_hbond_refined0.149
r_symmetry_vdw_refined0.133
r_xyhbond_nbd_refined0.123
r_nbtor_other0.091
r_chiral_restr0.07
r_bond_refined_d0.007
r_gen_planes_refined0.003
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_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 Atoms11872
Nucleic Acid Atoms
Solvent Atoms167
Heterogen Atoms257

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing