9NK1 | pdb_00009nk1

Prenylated-FMN maturase PhdC from Mycolicibacterium fortuitum bound to flavin mononucleotide

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		Previously acquired apo PhdC solution

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	1:2 protein (20mM bistris pH 7.2, 200mM KCl, 1mM MnCl2, 5% glycerol +FMN reconstitution) to condition (30% w/v PEG 5000 MME, 100 mM MES/ Sodium hydroxide pH 6.5, 200 mM ammonium sulfate)

Crystal Properties
Matthews coefficient	Solvent content
2.4	48.76

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.039	α = 90
b = 75.032	β = 90
c = 79.746	γ = 90

Symmetry
Space Group	I 2 2 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		2024-02-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL12-1	0.987	SSRL	BL12-1

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	1.23	47.97	84.2	0.035	0.038	0.015	0.999	18.3	5.6		44741

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	1.23	1.25	32.2		0.559	0.733	0.466	0.508	1.3	2.3

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	1.23	47.965	44079	2174	83.882	0.132	0.1308	0.1308	0.1481	0.1492	19.907

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]
-2.302			4.46		-2.158

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	17.302
r_lrange_other	16.206
r_dihedral_angle_2_deg	15.901
r_dihedral_angle_6_deg	14.849
r_scangle_it	12.855
r_scangle_other	12.594
r_dihedral_angle_3_deg	10.076
r_scbond_it	9.15
r_scbond_other	8.922
r_mcangle_other	7.843
r_mcangle_it	7.804
r_rigid_bond_restr	6.89
r_dihedral_angle_1_deg	6.645
r_mcbond_it	5.87
r_mcbond_other	5.791
r_angle_refined_deg	2.14
r_angle_other_deg	0.77
r_nbd_refined	0.228
r_symmetry_nbd_other	0.199
r_symmetry_nbd_refined	0.199
r_xyhbond_nbd_refined	0.19
r_nbd_other	0.187
r_nbtor_refined	0.179
r_symmetry_xyhbond_nbd_other	0.13
r_chiral_restr	0.124
r_symmetry_xyhbond_nbd_refined	0.12
r_symmetry_nbtor_other	0.089
r_metal_ion_refined	0.068
r_bond_refined_d	0.017
r_gen_planes_refined	0.012
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1182
Nucleic Acid Atoms
Solvent Atoms	134
Heterogen Atoms	41

Software

Software
Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
Aimless	data scaling
PHASER	phasing
Blu-Ice	data collection
Coot	model building