3GN5 | pdb_00003gn5

Structure of the E. coli protein MqsA (YgiT/b3021)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3GA8	PDB entries 3GA8 and 3FMY
experimental model	PDB	3FMY	PDB entries 3GA8 and 3FMY

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	277	0.1M Bis-Tris, 0.2M magnesium chloride hexahydrate, 25% PEG 3350, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.33	47.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.054	α = 90
b = 30.965	β = 106.6
c = 75.542	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	ADSC QUANTUM 270	toroidal focusing mirror	2009-03-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X6A	1.00	NSLS	X6A

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	2.15	50	99.4	0.074	12.9	3.2	15447	15349			25.2

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	2.15	2.19	99.7		0.271	4.85	3.1	759

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 entries 3GA8 and 3FMY	2.15	50	14577	14577	764	99.01	0.18475	0.18475	0.18201	0.18	0.23339	0.23	RANDOM	21.319

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]
0.96		-0.17	0.33		-1.38

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.694
r_dihedral_angle_3_deg	14.009
r_dihedral_angle_4_deg	13.083
r_scangle_it	5.795
r_dihedral_angle_1_deg	5.227
r_scbond_it	4.2
r_mcangle_it	2.615
r_mcbond_it	1.683
r_angle_refined_deg	1.225
r_angle_other_deg	0.88
r_mcbond_other	0.36
r_symmetry_vdw_other	0.237
r_nbd_refined	0.205
r_nbd_other	0.188
r_xyhbond_nbd_refined	0.173
r_nbtor_refined	0.172
r_symmetry_hbond_refined	0.16
r_symmetry_vdw_refined	0.14
r_nbtor_other	0.087
r_chiral_restr	0.074
r_bond_refined_d	0.011
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2052
Nucleic Acid Atoms
Solvent Atoms	153
Heterogen Atoms	8

Software

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