5KHK

HCN2 CNBD in complex with 2-aminopurine riboside-3', 5'-cyclic monophosphate (2-NH2-cPuMP)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1Q5O 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.6277200 mM NaCl, 0.1 mM sodium citrate pH 4.6, 12% PEG 400
Crystal Properties
Matthews coefficientSolvent content
2.2946.18

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 96.429α = 90
b = 96.429β = 90
c = 46.423γ = 90
Symmetry
Space GroupP 4 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M1000 um thick sensor2013-02-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-D1.033200APS23-ID-D

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12.0738.499.10.0670.99826.9913.8613521-349.461
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)
12.082.2194.40.7674.08

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 REPLACEMENTTHROUGHOUT1Q5O2.0738.41313269299.270.21830.21610.2614RANDOM47.952
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]
0.250.25-0.51
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.149
r_dihedral_angle_3_deg17.482
r_dihedral_angle_4_deg16.578
r_dihedral_angle_1_deg5.769
r_angle_refined_deg1.736
r_angle_other_deg0.8
r_chiral_restr0.091
r_bond_refined_d0.016
r_gen_planes_refined0.009
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.149
r_dihedral_angle_3_deg17.482
r_dihedral_angle_4_deg16.578
r_dihedral_angle_1_deg5.769
r_angle_refined_deg1.736
r_angle_other_deg0.8
r_chiral_restr0.091
r_bond_refined_d0.016
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1612
Nucleic Acid Atoms
Solvent Atoms52
Heterogen Atoms22

Software

Software
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing