2QSZ | pdb_00002qsz

Human nicotinamide riboside kinase 1 in complex with nicotinamide mononucleotide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2QSYPDB entry 2QSY

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP729120% PEG 3350, 0.2M Sodium phosphate monobasic, 0.15M D(+)sucrose, 0.1M HEPES pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.5551.74

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.921α = 90
b = 142.342β = 90
c = 62.434γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS2007-01-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E+ SUPERBRIGHT1.5418

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
11.93099.10.1386.44.819738
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)
1.91.9798.10.9014.21906

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 2QSY1.923.6419721103198.630.2190.2170.220.2550.26Reflections from isomorphous data of NRK1-ADP complex21.061
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]
0.030.28-0.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.625
r_dihedral_angle_4_deg18.199
r_dihedral_angle_3_deg13.255
r_dihedral_angle_1_deg5.757
r_angle_other_deg4.119
r_scangle_it2.905
r_mcangle_it2.84
r_scbond_it2.156
r_mcbond_it2.069
r_angle_refined_deg1.323
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.625
r_dihedral_angle_4_deg18.199
r_dihedral_angle_3_deg13.255
r_dihedral_angle_1_deg5.757
r_angle_other_deg4.119
r_scangle_it2.905
r_mcangle_it2.84
r_scbond_it2.156
r_mcbond_it2.069
r_angle_refined_deg1.323
r_nbd_other0.228
r_nbd_refined0.196
r_nbtor_refined0.177
r_symmetry_vdw_other0.168
r_symmetry_vdw_refined0.156
r_xyhbond_nbd_refined0.123
r_symmetry_hbond_refined0.117
r_nbtor_other0.108
r_chiral_restr0.079
r_bond_refined_d0.015
r_gen_planes_other0.007
r_gen_planes_refined0.005
r_bond_other_d
r_mcbond_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1559
Nucleic Acid Atoms
Solvent Atoms103
Heterogen Atoms35

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
PHASERphasing