5JRF | pdb_00005jrf

Crystal structure of the light-driven sodium pump KR2 bound with iodide ions

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	LIPIDIC CUBIC PHASE		293	in meso lipidic cubic phase crystallization

Crystal Properties
Matthews coefficient	Solvent content
3.31	62.86

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 40.506	α = 90
b = 83.749	β = 90
c = 234.102	γ = 90

Symmetry
Space Group	I 2 2 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	PIXEL	DECTRIS PILATUS 6M-F		2015-11-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	1.85	ESRF	ID23-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	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	2.35	60	99.2	0.126	0.999	10.25	6.73		26628

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	2.35	2.5	95.5		0.971	1.54	5.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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 (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	2.5	117.05	13612	720	99.88	0.1918	0.18978	0.2	0.22609	0.24	RANDOM	38.61

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]
0.16			-0.02		-0.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.965
r_dihedral_angle_4_deg	27.203
r_dihedral_angle_3_deg	14.469
r_long_range_B_refined	7.099
r_long_range_B_other	7.094
r_scangle_other	5.739
r_dihedral_angle_1_deg	5.466
r_mcangle_it	4.329
r_mcangle_other	4.328
r_scbond_it	3.732
r_scbond_other	3.73
r_mcbond_it	2.987
r_mcbond_other	2.971
r_angle_refined_deg	1.749
r_angle_other_deg	1.065
r_chiral_restr	0.101
r_bond_refined_d	0.016
r_gen_planes_refined	0.008
r_bond_other_d	0.003
r_gen_planes_other	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2122
Nucleic Acid Atoms
Solvent Atoms	49
Heterogen Atoms	89

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
SHELXCD	phasing
SHELXDE	phasing