2OKQ | pdb_00002okq

Crystal structure of unknown conserved ybaA protein from Shigella flexneri

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	295	0.5M Sodium chloride, 1.6M Sodium citrate tribasic dihydrate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.04	39.72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.843	α = 90
b = 61.843	β = 90
c = 137.32	γ = 90

Symmetry
Space Group	P 41 21 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	CCD	MARRESEARCH	mirrors	2006-10-29	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	MARRESEARCH	mirrors	2006-12-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-B	0.97857	APS	23-ID-B
2	SYNCHROTRON	APS BEAMLINE 21-ID-D	0.97869	APS	21-ID-D

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
1,2	1.8	25	99.7	0.045	36.1	6.1	25474	25474		-3

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)
	1.8	1.86	99.1		0.254	5.3	4.9	2467

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	1.8	20.39	24161	1255	99.79	0.18494	0.1828	0.18	0.22635	0.23	RANDOM	27.991

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]
0.84			0.84		-1.67

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.551
r_dihedral_angle_4_deg	20.992
r_dihedral_angle_3_deg	13.977
r_dihedral_angle_1_deg	6.521
r_scangle_it	4.286
r_scbond_it	2.611
r_mcangle_it	2.042
r_angle_refined_deg	1.279
r_mcbond_it	1.156
r_nbtor_refined	0.305
r_symmetry_vdw_refined	0.245
r_nbd_refined	0.212
r_symmetry_hbond_refined	0.168
r_xyhbond_nbd_refined	0.163
r_metal_ion_refined	0.163
r_chiral_restr	0.104
r_symmetry_metal_ion_refined	0.094
r_bond_refined_d	0.012
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2097
Nucleic Acid Atoms
Solvent Atoms	176
Heterogen Atoms	2

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SHARP	phasing