9QEX | pdb_00009qex

Structure of native leukocyte myeloperoxidase in complex with a truncated version of the Staphylococcal Peroxidase Inhibitor SPIN and thiocyanate at pH 7.5

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7Z53

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	295.15	0.1 M TRIS 7.5 pH (Buffer) 4 %(w/v) PEG 8K (Precipitant) 10 %(w/v) PEG 1K (Precipitant) 0.4 M KSCN (Salt)

Crystal Properties
Matthews coefficient	Solvent content
2.33	47.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 111.328	α = 90
b = 111.328	β = 90
c = 242.725	γ = 90

Symmetry
Space Group	P 43 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	213.15	PIXEL	DECTRIS EIGER X 16M	Toroidal mirror	2023-03-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.8856	ESRF	ID23-1

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	1.9	101.192	93.3	0.256	0.272	0.09	0.977	6.7	9.1		86444

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	1.9	2.101	66.4		3.456	3.729	1.372	0.241	1.7	7.7

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	THROUGHOUT	1.903	101.192	86440	4245	72.106	0.171	0.1682	0.1683	0.2158	0.216	RANDOM	38.466

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]
-0.128			-0.128		0.255

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.759
r_dihedral_angle_3_deg	14.04
r_dihedral_angle_2_deg	13.065
r_dihedral_angle_1_deg	6.865
r_lrange_it	6.4
r_lrange_other	6.351
r_scangle_it	4.725
r_scangle_other	4.724
r_scbond_it	3.196
r_scbond_other	3.196
r_mcangle_it	2.96
r_mcangle_other	2.96
r_mcbond_it	2.104
r_mcbond_other	2.104
r_angle_refined_deg	2.009
r_dihedral_angle_other_2_deg	0.779
r_angle_other_deg	0.66
r_symmetry_xyhbond_nbd_refined	0.542
r_nbd_refined	0.255
r_symmetry_nbd_refined	0.243
r_symmetry_nbd_other	0.191
r_nbd_other	0.19
r_nbtor_refined	0.181
r_xyhbond_nbd_refined	0.168
r_ncsr_local_group_2	0.147
r_symmetry_xyhbond_nbd_other	0.132
r_ncsr_local_group_3	0.107
r_chiral_restr	0.092
r_metal_ion_refined	0.088
r_symmetry_nbtor_other	0.085
r_ncsr_local_group_1	0.082
r_bond_refined_d	0.012
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10063
Nucleic Acid Atoms
Solvent Atoms	775
Heterogen Atoms	373

Software

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