8GYR | pdb_00008gyr

Crystal structure of a variable region segment of Leptospira host-interacting outer surface protein, LigA

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2MOG

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	295	23% PEG 3350, 260mM Potassium Iodide and 100mM Bis-Tris Propane

Crystal Properties
Matthews coefficient	Solvent content
2.45	49.86

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 34.219	α = 90
b = 63.905	β = 90
c = 171.839	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	MAR scanner 345 mm plate		2019-03-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.87	85.92	98.8	0.113	0.994	9.1	6.7		31943

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	1.87	1.91			0.759

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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	2MOG	1.87	85.92	30215	1527	98.35	0.20885	0.20757	0.21	0.23411	0.24	RANDOM	21.308

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]
-1.41			0.62		0.8

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.367
r_dihedral_angle_3_deg	13.311
r_dihedral_angle_4_deg	7.236
r_long_range_B_refined	6.19
r_dihedral_angle_1_deg	6.082
r_long_range_B_other	6.069
r_scangle_other	3.688
r_scbond_it	2.639
r_scbond_other	2.577
r_mcangle_other	2.032
r_mcangle_it	2.031
r_mcbond_it	1.41
r_mcbond_other	1.41
r_angle_refined_deg	1.337
r_angle_other_deg	1.02
r_chiral_restr	0.079
r_bond_refined_d	0.01
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2645
Nucleic Acid Atoms
Solvent Atoms	315
Heterogen Atoms	41

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
pointless	data scaling
BUCCANEER	phasing