2FGS | pdb_00002fgs

Crystal structure of Campylobacter jejuni YCEI protein, structural genomics

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1Y0G	PDB ENTRY 1Y0G

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	290	3.2M AMMONIUM SULFATE, 0.1M BIS-TRIS, pH 6.50, VAPOR DIFFUSION, SITTING DROP, temperature 290K

Crystal Properties
Matthews coefficient	Solvent content
6.1	78.25

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 179.535	α = 90
b = 179.535	β = 90
c = 50.577	γ = 120

Symmetry
Space Group	P 6 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	IMAGE PLATE	RIGAKU RAXIS IV	MIRRORS	2005-12-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200	1.5418

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	2.9	50	99.8	0.124	0.088	6.2	14.1	11129	11129

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)
	2.9	3	100		0.398	0.46	2.2	13.8	1092

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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 1Y0G	2.9	20	10524	10524	531	99.71	0.262	0.24492	0.24314	0.2432	0.27986	0.234	RANDOM	69.73

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]
3.65	1.82		3.65		-5.47

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.183
r_dihedral_angle_4_deg	36.512
r_dihedral_angle_3_deg	19.925
r_scangle_it	7.164
r_dihedral_angle_1_deg	6.373
r_scbond_it	4.537
r_mcangle_it	2.977
r_mcbond_it	1.575
r_angle_refined_deg	1.25
r_nbtor_refined	0.306
r_nbd_refined	0.19
r_xyhbond_nbd_refined	0.156
r_symmetry_vdw_refined	0.144
r_symmetry_hbond_refined	0.11
r_chiral_restr	0.087
r_bond_refined_d	0.008
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1328
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	5

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement