2HVE

S120G mutant of human nucleoside diphosphate kinase A complexed with ADP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1UCNPDB ENTRY 1UCN

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP62932.4 M AMMONIUM SULPHATE, 10 MM ADP, 20 MM MGCL2, 4 MM DTT, 0.1 M MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.956.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 114.824α = 90
b = 114.824β = 90
c = 89.719γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2004-09-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM30A0.980ESRFBM30A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.4024097.10.121.410.9220882208849.109
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.4022.5386.70.448.4

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 1UCN2.402402208822088119297.090.220780.220780.217840.27725RANDOM48.111
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]
-0.06-0.060.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.714
r_dihedral_angle_4_deg20.984
r_dihedral_angle_3_deg14.151
r_dihedral_angle_1_deg5.948
r_angle_other_deg2.315
r_scangle_it1.878
r_scbond_it1.48
r_angle_refined_deg1.256
r_mcbond_it1.027
r_mcangle_it0.94
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.714
r_dihedral_angle_4_deg20.984
r_dihedral_angle_3_deg14.151
r_dihedral_angle_1_deg5.948
r_angle_other_deg2.315
r_scangle_it1.878
r_scbond_it1.48
r_angle_refined_deg1.256
r_mcbond_it1.027
r_mcangle_it0.94
r_symmetry_vdw_refined0.441
r_nbd_other0.207
r_nbd_refined0.197
r_symmetry_vdw_other0.192
r_nbtor_refined0.174
r_xyhbond_nbd_refined0.165
r_symmetry_hbond_refined0.152
r_nbtor_other0.087
r_chiral_restr0.068
r_mcbond_other0.025
r_bond_refined_d0.009
r_gen_planes_refined0.003
r_gen_planes_other0.003
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3588
Nucleic Acid Atoms
Solvent Atoms151
Heterogen Atoms81

Software

Software
Software NamePurpose
MAR345data collection
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling