4BGC | pdb_00004bgc

T1 domain of the renal potassium channel Kv1.3

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1QDW	PDB ENTRY 1QDW

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.5		WE WANTED TO USE THE PROTEIN IN 150 MM POTASSIUM PHOSPHATE BUFFER PH 6.5 IN 5 MM NMR TUBES FOR CHARACTERIZATION USING NMR SPECTROSCOPY. DURING TESTING, WE OBSERVED THE FORMATION OF CRYSTALS IN THE NMR TUBES. AN INITIAL TEST OF THE CRYSTALS SHOWED AN EXCELLENT DIFFRACTION PATTERN, SO WE DECIDED TO CONTINUE WITH CRYSTALLIZATION OPTIMIZATION IN NMR TUBES, RESULTING IN VERY GOOD CRYSTALS

Crystal Properties
Matthews coefficient	Solvent content
2.2	43.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.74	α = 90
b = 59.74	β = 90
c = 62.33	γ = 90

Symmetry
Space Group	I 4

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	MARRESEARCH	DYNAMICALLY BENDABLE MIRROR	2005-04-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA		SLS	X10SA

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	1.2	45	99.2	0.05	17	3.7		33942

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	1.2	1.3	98.5		0.16	8.6	3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1QDW	1.2	18.97	29377	1537	90.42	0.16499	0.16297	0.17	0.20463	RANDOM	12.573

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]
0.22			0.22		-0.43

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.199
r_dihedral_angle_4_deg	18.82
r_sphericity_free	13.454
r_dihedral_angle_3_deg	12.774
r_scangle_it	6.154
r_sphericity_bonded	5.726
r_dihedral_angle_1_deg	4.949
r_scbond_it	4.859
r_mcangle_it	3.632
r_mcbond_it	2.873
r_rigid_bond_restr	2.566
r_angle_refined_deg	2.205
r_mcbond_other	1.281
r_angle_other_deg	1.18
r_symmetry_vdw_refined	0.366
r_symmetry_vdw_other	0.364
r_symmetry_hbond_refined	0.284
r_nbd_refined	0.252
r_nbd_other	0.22
r_nbtor_refined	0.199
r_xyhbond_nbd_refined	0.185
r_chiral_restr	0.155
r_nbtor_other	0.107
r_bond_refined_d	0.028
r_gen_planes_refined	0.013
r_bond_other_d	0.002
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	859
Nucleic Acid Atoms
Solvent Atoms	144
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing