9T54 | pdb_00009t54

Coproheme decarboxylase H117A mutant from Listeria monocytogenes in complex with iron coproporphyrin III

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		295	0.2 M Ammonium iodide 20 % w/v PEG 3350 1 mM Cyanide 5 mg/mL protein

Crystal Properties
Matthews coefficient	Solvent content
2.64	53.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.429	α = 90
b = 129.3	β = 106.048
c = 78.651	γ = 90

Symmetry
Space Group	P 1 21 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 4M		2025-09-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE MASSIF-3	0.9677	ESRF	MASSIF-3

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	2.19	65.254	98.51	0.3247	0.3498	0.129	0.986	6.92	7.2		76424			36.2

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	2.19	2.268	96.78		2.636	2.832	1.028	0.405	1.16	7.4

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.194	65.254	76213	1754	97.965	0.183	0.1804	0.1891	0.2061	0.2203	RANDOM	44.79

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]
-12.214		-16.548	35.142		-22.928

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.877
r_dihedral_angle_6_deg	14.596
r_lrange_it	10.392
r_dihedral_angle_2_deg	9.74
r_scangle_it	8.79
r_dihedral_angle_1_deg	7.087
r_scbond_it	6.984
r_mcangle_it	6.869
r_mcbond_it	5.639
r_angle_refined_deg	1.997
r_symmetry_nbd_refined	0.336
r_nbtor_refined	0.311
r_nbd_refined	0.226
r_symmetry_xyhbond_nbd_refined	0.216
r_xyhbond_nbd_refined	0.182
r_chiral_restr	0.136
r_ncsr_local_group_3	0.1
r_ncsr_local_group_8	0.097
r_ncsr_local_group_9	0.091
r_ncsr_local_group_2	0.088
r_ncsr_local_group_6	0.088
r_ncsr_local_group_1	0.085
r_ncsr_local_group_7	0.084
r_ncsr_local_group_4	0.081
r_ncsr_local_group_10	0.081
r_ncsr_local_group_5	0.079
r_bond_refined_d	0.012
r_gen_planes_refined	0.012

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10046
Nucleic Acid Atoms
Solvent Atoms	35
Heterogen Atoms	245

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
DIALS	data reduction
gemmi	data extraction
PHASER	phasing
Coot	model building