Experiment: 9YLD

Crystal structure of reduced as-isolated Fe(II)Fe(II) Streptomyces griseoflavus HrmI in complex with L-lysine

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		Experimentally phased model using SeMet incorporation

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	294	0.1 M Tris pH 7.0, 0.1 M MgCl2, 15% PEG 8000

Crystal Properties
Matthews coefficient	Solvent content
2.37	48.06

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 106.028	α = 90
b = 74.546	β = 103.356
c = 51.148	γ = 90

Symmetry
Space Group	C 1 2 1

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	Horizontal pre-focus bimorph mirror & KB bimorph mirrors	2025-02-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS-II BEAMLINE 17-ID-2	0.979342	NSLS-II	17-ID-2

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	1.551	40.84	92.63	0.1225	0.1336	0.05259	0.997	9.49	6.3		51906			15.01

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	1.551	1.607	99.51		1.071	1.16	0.4425	0.416	1.93	6.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.551	40.84	1.34	51904	2539	92.63	0.1969	0.1959	0.1953	0.2163	0.2167	20.86

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
f_dihedral_angle_d	5.255
f_angle_d	0.7548
f_chiral_restr	0.0487
f_plane_restr	0.0069
f_bond_d	0.0049

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2709
Nucleic Acid Atoms
Solvent Atoms	315
Heterogen Atoms	13

Software

Software
Software Name	Purpose
PHENIX	refinement
PHENIX	phasing
autoPROC	data reduction
autoPROC	data scaling