31HE | pdb_000031he

Xray crystal structure of PtsM receptor binding protein

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		290	0.1 M MgCl2, 0.1 M Na HEPES pH 7.5, 10% w/v PEG 4000

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 161.59	α = 90
b = 67.37	β = 99.77
c = 51.89	γ = 90

Symmetry
Space Group	C 1 2 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	PIXEL	DECTRIS EIGER2 XE 16M		2019-01-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9762	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.42	46.81	99.8	1	9.4	6.5		103206

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.42	1.44			0.3

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	SAD	FREE R-VALUE	1.42	46.789	103206	5081	99.788	0.186	0.1852	0.1855	0.2017	0.2016	20.608

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]
0.183		-0.91	-0.264		0.372

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.15
r_dihedral_angle_3_deg	11.546
r_dihedral_angle_1_deg	7.393
r_lrange_it	7.145
r_lrange_other	7.127
r_dihedral_angle_4_deg	6.674
r_scangle_it	5.59
r_scangle_other	5.589
r_scbond_other	3.842
r_scbond_it	3.839
r_mcangle_it	2.793
r_mcangle_other	2.793
r_mcbond_it	2.023
r_mcbond_other	2.021
r_angle_refined_deg	1.881
r_angle_other_deg	1.565
r_nbd_refined	0.215
r_symmetry_nbd_other	0.189
r_nbtor_refined	0.186
r_nbd_other	0.173
r_symmetry_nbd_refined	0.166
r_xyhbond_nbd_refined	0.162
r_metal_ion_refined	0.111
r_chiral_restr	0.101
r_symmetry_xyhbond_nbd_refined	0.091
r_symmetry_nbtor_other	0.084
r_bond_refined_d	0.014
r_gen_planes_refined	0.011
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2579
Nucleic Acid Atoms
Solvent Atoms	239
Heterogen Atoms	5

Software

Software
Software Name	Purpose
REFMAC	refinement
FAST_DP	data reduction
FAST_DP	data scaling
PHASER	phasing
SHELXDE	phasing
BUCCANEER	model building