4NVP | pdb_00004nvp

Structure of the cyclic nucleotide-binding domain of HCN4 channel complexed with 7-CH-cAMP

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3U11	PDB ENTRY 3U11_A

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	277	HCN4 521-723 (10 mg mL-1) and 7-CH-cAMP 0.5mM were mixed in a 2:1 ratio with 100 mM TrisCl pH 8.0, 20 % PEG4000 (w/v), VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.38	48.39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 96.01	α = 90
b = 96.01	β = 90
c = 50.17	γ = 90

Symmetry
Space Group	P 4 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MARMOSAIC 225 mm CCD	bending magnet; bent collimating mirror and toroid	2013-10-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM14	0.97372	ESRF	BM14

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	2.5	50.17	100	0.08	16.4	8.1	8568	8568		5	33.2

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	2.5	2.64	99.9		0.45	4.3	7.7	1215

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 3U11_A	2.5	44.47	8148	8141	406	99.92	0.20117	0.19799	0.2034	0.27031	0.2774	RANDOM	42.441

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]
-0.05			-0.05		0.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.176
r_dihedral_angle_3_deg	19.842
r_dihedral_angle_4_deg	13.757
r_long_range_B_refined	8.003
r_long_range_B_other	8.001
r_dihedral_angle_1_deg	6.32
r_scangle_other	5.814
r_mcangle_other	4.421
r_mcangle_it	4.42
r_scbond_it	3.6
r_scbond_other	3.598
r_mcbond_it	2.807
r_mcbond_other	2.786
r_angle_refined_deg	1.504
r_angle_other_deg	0.78
r_chiral_restr	0.082
r_bond_refined_d	0.011
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1661
Nucleic Acid Atoms
Solvent Atoms	37
Heterogen Atoms	22

Software

Software
Software Name	Purpose
ADSC	data collection
AMoRE	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling