7KL8 | pdb_00007kl8

Structure of F420 binding protein Rv1558 from Mycobacterium tuberculosis with F420 bound

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3R5R

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		292	0.1 M Sodium citrate pH 5.8, 0.5 M Ammonium sulfate, 1 M Lithium sulfate, and 3 % Glycerol (v/v)

Crystal Properties
Matthews coefficient	Solvent content
6.47	80.99

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 169.544	α = 90
b = 169.544	β = 90
c = 169.544	γ = 90

Symmetry
Space Group	P 43 3 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	PIXEL	DECTRIS EIGER X 16M		2019-07-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX2	0.953719973564	Australian Synchrotron	MX2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim 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	2.469	48.99	99.7	0.187	0.028	1	28.5	78.5		30473

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.469	2.558	97.54		5.963	0.945	0.416	1.1

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	3R5R	2.469	48.99	28938	1595	99.8	0.20106	0.20003	0.21	0.22012	0.23	RANDOM	83.23

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
r_dihedral_angle_2_deg	34.573
r_dihedral_angle_3_deg	14.91
r_dihedral_angle_4_deg	14.244
r_long_range_B_other	7.481
r_long_range_B_refined	7.466
r_dihedral_angle_1_deg	5.49
r_scangle_other	4.637
r_mcangle_it	3.276
r_mcangle_other	3.275
r_scbond_it	3.225
r_scbond_other	2.991
r_mcbond_it	2.095
r_mcbond_other	2.095
r_angle_refined_deg	1.248
r_angle_other_deg	0.996
r_chiral_restr	0.069
r_bond_refined_d	0.009
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	2216
Nucleic Acid Atoms
Solvent Atoms	29
Heterogen Atoms	145

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing