3BPZ

HCN2-I 443-460 E502K in the presence of cAMP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1Q43PDB ENTRY 1Q43 WITHOUT LIGAND OR E502 SIDE-CHAIN

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION4.6279PEG 400, SODIUM CITRATE, SODIUM CHLORIDE, DTT, HEPES, 5 mM CAMP, pH 4.6, VAPOR DIFFUSION, temperature 279K
Crystal Properties
Matthews coefficientSolvent content
2.9658.39

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 123.899α = 90
b = 134.264β = 90
c = 134.359γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDADSC QUANTUM 4The X26C beamline optics consist of a channel-cut Si(111) crystal monochromator followed by a doubly focusing toroidal mirror2003-04-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X26C0.92NSLSX26C

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
11.6550990.07317.613.9133824132486
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)
1.651.7191.50.418.7

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1Q43 WITHOUT LIGAND OR E502 SIDE-CHAIN1.6530133818125766666098.960.191390.190120.21578RANDOM17.93
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]
-0.290.080.21
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.791
r_dihedral_angle_3_deg12.237
r_dihedral_angle_4_deg10.47
r_dihedral_angle_1_deg5.048
r_scangle_it3.463
r_scbond_it2.117
r_angle_refined_deg1.315
r_mcangle_it1.314
r_mcbond_it0.731
r_nbtor_refined0.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.791
r_dihedral_angle_3_deg12.237
r_dihedral_angle_4_deg10.47
r_dihedral_angle_1_deg5.048
r_scangle_it3.463
r_scbond_it2.117
r_angle_refined_deg1.315
r_mcangle_it1.314
r_mcbond_it0.731
r_nbtor_refined0.31
r_nbd_refined0.204
r_symmetry_vdw_refined0.173
r_xyhbond_nbd_refined0.125
r_symmetry_hbond_refined0.113
r_chiral_restr0.087
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6121
Nucleic Acid Atoms
Solvent Atoms1044
Heterogen Atoms88

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
CBASSdata collection