7BK8 | pdb_00007bk8

X-ray crystal structure of Pseudomonas aeruginosa MagC

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6.5	293	30% w/v PEG6000, 100 mM Citrate pH 6.5

Crystal Properties
Matthews coefficient	Solvent content
2.02	39.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 110.737	α = 90
b = 110.737	β = 90
c = 41.11	γ = 120

Symmetry
Space Group	H 3

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 2M		2016-06-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	LNLS BEAMLINE W01B-MX2	1.458680	LNLS	W01B-MX2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	CC (Half)	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	1.74	37.79	98.4	0.045	1	26.91	6.6		18977		-3	31.783

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.74	1.85	93.7		0.569	0.889	3	4.9

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	AB INITIO PHASING	FREE R-VALUE	1.74	37.785	18977	1868	98.403	0.196	0.1932	0.2	0.2219	0.23	39.74

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]
0.416	0.208		0.416		-1.349

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.329
r_dihedral_angle_4_deg	15.832
r_dihedral_angle_3_deg	12.833
r_lrange_it	7.374
r_lrange_other	7.371
r_dihedral_angle_1_deg	6.44
r_scangle_other	4.661
r_scangle_it	4.656
r_mcangle_it	3.426
r_mcangle_other	3.424
r_scbond_it	3.093
r_scbond_other	3.044
r_mcbond_it	2.352
r_mcbond_other	2.346
r_angle_other_deg	1.271
r_angle_refined_deg	1.267
r_symmetry_nbd_other	0.212
r_nbd_refined	0.209
r_nbd_other	0.197
r_symmetry_xyhbond_nbd_refined	0.197
r_symmetry_nbd_refined	0.188
r_nbtor_refined	0.171
r_xyhbond_nbd_refined	0.14
r_symmetry_nbtor_other	0.076
r_chiral_restr	0.058
r_bond_refined_d	0.007
r_gen_planes_refined	0.004
r_bond_other_d
r_gen_planes_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1545
Nucleic Acid Atoms
Solvent Atoms	82
Heterogen Atoms	5

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
Arcimboldo	phasing