9FPP | pdb_00009fpp

FGD2 (Rv0132c) from Mycobacterium tuberculosis with cofactor F420 crystallised with Anderson-Evans polyoxotungstate

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	9FP4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	277.15	0.12M Monosaccharides, 0.1M buffer system 1 pH 6.5 (MES imidazole), 37.5% precipitant mix 4 Morpheus condition F4

Crystal Properties
Matthews coefficient	Solvent content
2.12	41.88

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 87.31	α = 90
b = 89.311	β = 90
c = 155.634	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	99	PIXEL	DECTRIS EIGER2 XE 16M		2021-11-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9763	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	2.35	77.82	100	0.282	0.293	0.08	0.996	6.2	13.1		51484

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.35	2.42	100		1.04	1.088	0.317	0.895	2.1	11.5

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	MOLECULAR REPLACEMENT	THROUGHOUT	2.35	77.82	51398	2612	99.959	0.213	0.2105	0.2113	0.2508	0.2515	21.907

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]
-0.776			-1.287		2.063

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.606
r_dihedral_angle_3_deg	13.954
r_dihedral_angle_2_deg	8.049
r_dihedral_angle_1_deg	6.734
r_lrange_it	4.895
r_scangle_it	2.496
r_angle_refined_deg	1.889
r_scbond_it	1.758
r_mcangle_it	1.138
r_metal_ion_refined	0.763
r_mcbond_it	0.67
r_nbtor_refined	0.309
r_symmetry_nbd_refined	0.303
r_symmetry_xyhbond_nbd_refined	0.221
r_nbd_refined	0.211
r_xyhbond_nbd_refined	0.208
r_chiral_restr	0.122
r_ncsr_local_group_4	0.081
r_ncsr_local_group_1	0.077
r_ncsr_local_group_6	0.077
r_ncsr_local_group_3	0.068
r_ncsr_local_group_5	0.053
r_ncsr_local_group_2	0.052
r_bond_refined_d	0.008
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9784
Nucleic Acid Atoms
Solvent Atoms	721
Heterogen Atoms	345

Software

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