3BPZ | pdb_00003bpz

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

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1Q43	PDB ENTRY 1Q43 WITHOUT LIGAND OR E502 SIDE-CHAIN

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	4.6	279	PEG 400, SODIUM CITRATE, SODIUM CHLORIDE, DTT, HEPES, 5 mM CAMP, pH 4.6, VAPOR DIFFUSION, temperature 279K

Crystal Properties
Matthews coefficient	Solvent content
2.96	58.39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 123.899	α = 90
b = 134.264	β = 90
c = 134.359	γ = 90

Symmetry
Space Group	C 2 2 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	110	CCD	ADSC QUANTUM 4	The X26C beamline optics consist of a channel-cut Si(111) crystal monochromator followed by a doubly focusing toroidal mirror	2003-04-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X26C	0.92	NSLS	X26C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.65	50	99	0.073	17.6	13.9	133824	132486

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.65	1.71	91.5		0.41		8.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1Q43 WITHOUT LIGAND OR E502 SIDE-CHAIN	1.65	30	133818	125766	6660	98.96	0.19139	0.19012	0.19	0.21578	0.21	RANDOM	17.93

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]
-0.29			0.08		0.21

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.791
r_dihedral_angle_3_deg	12.237
r_dihedral_angle_4_deg	10.47
r_dihedral_angle_1_deg	5.048
r_scangle_it	3.463
r_scbond_it	2.117
r_angle_refined_deg	1.315
r_mcangle_it	1.314
r_mcbond_it	0.731
r_nbtor_refined	0.31
r_nbd_refined	0.204
r_symmetry_vdw_refined	0.173
r_xyhbond_nbd_refined	0.125
r_symmetry_hbond_refined	0.113
r_chiral_restr	0.087
r_bond_refined_d	0.011
r_gen_planes_refined	0.006
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 Atoms	Number
Protein Atoms	6121
Nucleic Acid Atoms
Solvent Atoms	1044
Heterogen Atoms	88

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection