2YLN

Crystal structure of the L-cystine solute receptor of Neisseria gonorrhoeae in the closed conformation

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		4		1.6 M AMMONIUM SULFATE, 100 MM NA-CITRATE PH 4.0.

Crystal Properties
Matthews coefficient	Solvent content
1.37	9.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 35.73	α = 90
b = 63.43	β = 96.89
c = 44.65	γ = 90

Symmetry
Space Group	P 1 21 1

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		2010-02-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.2		BESSY	14.2

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	1.12	30.96	99	0.06	16.3	3.8		75069		-3	7.42

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	1.12	1.15	90.7		0.54	2.3	2.7

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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 3ZSF	1.12	30.96	71314	3754	100	0.11087	0.10923	0.12	0.14176	0.15	RANDOM	8.232

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]
-0.31		-0.27	0.32		-0.07

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.99
r_dihedral_angle_4_deg	25.197
r_dihedral_angle_3_deg	12.279
r_scangle_it	7.305
r_dihedral_angle_1_deg	7.185
r_scbond_it	5.048
r_mcangle_it	3.031
r_mcbond_it	2.185
r_angle_refined_deg	2.137
r_rigid_bond_restr	2.078
r_angle_other_deg	1.067
r_mcbond_other	0.772
r_chiral_restr	0.12
r_bond_refined_d	0.023
r_gen_planes_refined	0.013
r_gen_planes_other	0.003
r_bond_other_d	0.001
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1806
Nucleic Acid Atoms
Solvent Atoms	275
Heterogen Atoms	60

Software

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