4LGW | pdb_00004lgw

Crystal structure of Escherichia coli SdiA in the space group P6522

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.2	287	0.1M 4-(2-Hydroxyethyl)piperazine-1-ethanesulfonic acid, 0.2M Lithium sulfate, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 287K

Crystal Properties
Matthews coefficient	Solvent content
5.27	76.64

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 130.474	α = 90
b = 130.474	β = 90
c = 125.234	γ = 120

Symmetry
Space Group	P 65 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		CCD	RAYONIX MX225HE			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL41XU	1.0000	SPring-8	BL41XU

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.7	30	99.8	0.058	41.9	10.1	17821	17785

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.7		100		0.398	5.5	10.2	1726

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	2.7	30	17821	16858	902	99.5	0.23201	0.22999	0.23	0.27121	0.27	RANDOM	56.035

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]
0.9	0.45		0.9		-1.35

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.631
r_dihedral_angle_4_deg	23.754
r_dihedral_angle_3_deg	20.735
r_dihedral_angle_1_deg	6.099
r_scangle_it	3.079
r_scbond_it	1.905
r_angle_refined_deg	1.512
r_mcangle_it	1.4
r_mcbond_it	0.784
r_nbtor_refined	0.316
r_nbd_refined	0.24
r_symmetry_vdw_refined	0.194
r_symmetry_hbond_refined	0.186
r_chiral_restr	0.115
r_xyhbond_nbd_refined	0.112
r_bond_refined_d	0.013
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1958
Nucleic Acid Atoms
Solvent Atoms	52
Heterogen Atoms	6

Software

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