4APS | pdb_00004aps

Crystal structure of a POT family peptide transporter in an inward open conformation.

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.5		26 % PEG 400, 0.1 M MES PH 6.50, 0.03 M MGCL2 0.001 M CDCL2

Crystal Properties
Matthews coefficient	Solvent content
5.4	77

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 89.39	α = 90
b = 112.99	β = 90
c = 215.49	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	277	CCD	ADSC CCD	KIRKPATRICK BAEZ BIMORPH MIRROR PAIR FOR HORIZONTAL AND VERTICAL FOCUSSING	2009-07-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I02		Diamond	I02

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	3.3	82	99	0.1	5.1	3.5		33300		2	127.67

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	3.3	3.4	99		1.11	1.1	3.5

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 (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MIRAS	THROUGHOUT	NONE	3.3	22.62	27943	1421	83.45	0.2731	0.2722	0.32	0.2895	0.34	RANDOM	140.73

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]
-9.5188			-17.3228		26.8416

RMS Deviations
Key	Refinement Restraint Deviation
t_other_torsion	18.88
t_omega_torsion	3.14
t_angle_deg	0.98
t_bond_d	0.01
t_dihedral_angle_d
t_incorr_chiral_ct
t_pseud_angle
t_trig_c_planes
t_gen_planes
t_it

RMS Deviations
Key	Refinement Restraint Deviation
t_other_torsion	18.88
t_omega_torsion	3.14
t_angle_deg	0.98
t_bond_d	0.01
t_dihedral_angle_d
t_incorr_chiral_ct
t_pseud_angle
t_trig_c_planes
t_gen_planes
t_it
t_nbd
t_improper_torsion
t_chiral_improper_torsion
t_sum_occupancies
t_utility_distance
t_utility_angle
t_utility_torsion
t_ideal_dist_contact

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6890
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	1

Software

Software
Software Name	Purpose
BUSTER	refinement
MOSFLM	data reduction
Aimless	data scaling
SHARP	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.