6PZJ | pdb_00006pzj

Structure of the N-terminal domain (residues 43-304) of Methyl-accepting chemotaxis protein from Leptospira interrogans serogroup Icterohaemorrhagiae serovar Copenhageni (strain Fiocruz L1-130)

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	9.5	290	RigakuReagents JCSG+ screen A7: 20% (w/V) PEG 8000, 100mM CHES / NaOH pH 9.5: LpinA.18975.a.B2.PW38653 at 19.51mg/ml: cryo: 20% EG in 2 steps: tray 310977 a7: puck hqx5-3. For phasing: Microlytic MCSG1 screen condition H3: 20% (w/V) PEG 3350, 200mM Lithium acetate: LpinA.18975.a.B2.PW38653 at 19.51mg/ml. A crystal from this condition was soaked for 15sec in a mix of 90% reservoir and 10% 2.5M NaI in EG, and for another 15sec in a mix of 80% reservoir and 20% 2.5M NaI in EG, and flash frozen for in-house data collection: tray 310978 h3: puck hqx5-12

Crystal Properties
Matthews coefficient	Solvent content
2.4	48.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.09	α = 90
b = 72.09	β = 90
c = 116.89	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	RAYONIX MX-300		2019-07-18	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	RIGAKU SATURN 944+		2019-07-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F
2	ROTATING ANODE	RIGAKU FR-E+ SUPERBRIGHT	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	1.75	38.416	100	0.046	0.048	1	30.66	11.48		31892			32.859

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.75	1.8	100		0.599	0.641	0.875	3.18	7.958

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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	1.75	38.416	1.35	31821	1984	99.98	0.1677	0.1652	0.1731	0.2053	0.2137	0	32.9902

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	12.224
f_angle_d	0.932
f_chiral_restr	0.067
f_bond_d	0.008
f_plane_restr	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2132
Nucleic Acid Atoms
Solvent Atoms	223
Heterogen Atoms	9

Software

Software
Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
PHASER	phasing
PARROT	phasing
ARP/wARP	model building
Coot	model building