6TIF | pdb_00006tif

ReoM- Listeria monocytogenes

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5US5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.2	293	0.1 M phosphate/citrate 0.2 lithium sulphate 20 % w/v PEG 1000

Crystal Properties
Matthews coefficient	Solvent content
2.12	41.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 38.788	α = 90
b = 58.619	β = 90
c = 74.449	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	PIXEL	DECTRIS EIGER2 XE 16M		2018-05-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.976250	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	1.6	74.45	99.8	0.986	8.2	4.8		23059

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	1.6	1.63			0.62	2.2

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	5US5	1.6	37.252	23008	960	99.731	0.156	0.153	0.17	0.2137	0.21	25.171

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]
1.516			-2.119		0.603

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.887
r_dihedral_angle_4_deg	18.785
r_dihedral_angle_3_deg	13.152
r_scangle_it	6.224
r_lrange_it	6.152
r_lrange_other	6.117
r_scangle_other	5.699
r_dihedral_angle_1_deg	5.631
r_mcangle_it	5.082
r_mcangle_other	5.082
r_scbond_it	5.018
r_scbond_other	4.742
r_mcbond_it	4.386
r_mcbond_other	4.372
r_rigid_bond_restr	3.609
r_angle_refined_deg	1.6
r_angle_other_deg	1.458
r_nbd_other	0.236
r_nbd_refined	0.227
r_symmetry_nbd_refined	0.207
r_symmetry_nbd_other	0.202
r_xyhbond_nbd_refined	0.178
r_nbtor_refined	0.174
r_symmetry_xyhbond_nbd_refined	0.169
r_chiral_restr	0.082
r_symmetry_nbtor_other	0.075
r_bond_refined_d	0.01
r_gen_planes_refined	0.008
r_symmetry_xyhbond_nbd_other	0.007
r_bond_other_d	0.006
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1394
Nucleic Acid Atoms
Solvent Atoms	94
Heterogen Atoms	20

Software

Software
Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
Aimless	data scaling
PHASER	phasing