5KHI

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


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.5277200 mM NaCl, 0.1 mM sodium citrate pH 5.5, 18% PEG 400
Crystal Properties
Matthews coefficientSolvent content
2.346.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 96.278α = 90
b = 96.278β = 90
c = 46.763γ = 90
Symmetry
Space GroupP 4 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M1000 um thick sensor2012-11-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-D0.979440APS23-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
12.131.799.50.0580.99818.67.0413266-354.763
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)
12.12.23990.8282.68

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 REPLACEMENTTHROUGHOUT1Q5O2.131.71254164899.050.20290.20060.2489RANDOM58.676
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]
-0.02-0.020.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.538
r_dihedral_angle_3_deg17.265
r_dihedral_angle_4_deg13.834
r_dihedral_angle_1_deg5.572
r_angle_refined_deg1.467
r_angle_other_deg0.748
r_chiral_restr0.079
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.538
r_dihedral_angle_3_deg17.265
r_dihedral_angle_4_deg13.834
r_dihedral_angle_1_deg5.572
r_angle_refined_deg1.467
r_angle_other_deg0.748
r_chiral_restr0.079
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1623
Nucleic Acid Atoms
Solvent Atoms39
Heterogen Atoms21

Software

Software
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing