5KHJ

HCN2 CNBD in complex with uridine-3', 5'-cyclic monophosphate (cUMP)


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, 13% PEG 400
Crystal Properties
Matthews coefficientSolvent content
2.1843.71

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.486α = 90
b = 89.925β = 90
c = 98.421γ = 90
Symmetry
Space GroupP 2 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M1000 um thick sensor2012-10-31MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-D1.033180APS23-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
12.0128.6995.10.0630.9937.351.5427507-336.11
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)
12.012.1394.30.3532

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 REPLACEMENTTHROUGHOUT1Q5O2.0128.6926112139597.340.1850.18140.2518RANDOM32.349
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]
-0.850.290.57
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.789
r_dihedral_angle_4_deg18.512
r_dihedral_angle_3_deg15.461
r_dihedral_angle_1_deg6.328
r_angle_refined_deg1.799
r_angle_other_deg0.872
r_chiral_restr0.1
r_bond_refined_d0.017
r_gen_planes_refined0.009
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.789
r_dihedral_angle_4_deg18.512
r_dihedral_angle_3_deg15.461
r_dihedral_angle_1_deg6.328
r_angle_refined_deg1.799
r_angle_other_deg0.872
r_chiral_restr0.1
r_bond_refined_d0.017
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 Atoms3160
Nucleic Acid Atoms
Solvent Atoms314
Heterogen Atoms40

Software

Software
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing