3JYB | pdb_00003jyb

Crystal Structure of the RetS periplasmic domain

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	3	291	22.5% PEG 3350, 0.1M citric acid, 10% glycerol, pH 3.0, VAPOR DIFFUSION, SITTING DROP, temperature 291.0K

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.164	α = 90
b = 67.193	β = 90
c = 86.214	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	100	CCD	ADSC QUANTUM 315	SAGITALLY FOCUSED Si(111)	2008-11-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A	0.97900	NSLS	X29A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2.04	30	99.9	0.114	0.114	26.32	13.1	19459	19459		-3	18.747

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.04	2.11	100		0.444	0.444	4.65	8.9

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	2.04	29.62	17870	975	100	0.20119	0.19937	0.2102	0.23491	0.2432	RANDOM	18.747

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]
-0.32			0.35		-0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.181
r_dihedral_angle_4_deg	16.425
r_dihedral_angle_3_deg	15.143
r_dihedral_angle_1_deg	6.281
r_scangle_it	1.835
r_angle_refined_deg	1.119
r_scbond_it	1.076
r_mcangle_it	0.743
r_mcbond_it	0.513
r_nbtor_refined	0.304
r_nbd_refined	0.188
r_symmetry_vdw_refined	0.169
r_symmetry_hbond_refined	0.128
r_xyhbond_nbd_refined	0.117
r_chiral_restr	0.072
r_bond_refined_d	0.007
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2298
Nucleic Acid Atoms
Solvent Atoms	104
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	model building
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
REFMAC	phasing
HKL-2000	data collection