9QE3 | pdb_00009qe3

Structure of native leukocyte myeloperoxidase in complex with a truncated version of the Staphylococcal Peroxidase Inhibitor SPIN and selenocyanate at pH 5.5

X-RAY DIFFRACTION

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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	5.5	295.15	0.1 M Na Acet 5.5 pH (Buffer) 6 %(w/v) PEG 8K (Precipitant) 10 %(w/v) PEG 1K (Precipitant) 0.4 M KSeCN (Salt)

Crystal Properties
Matthews coefficient	Solvent content
2.31	46.75

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 110.507	α = 90
b = 110.507	β = 90
c = 241.574	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	2.058	19.89	94.3	0.353	0.386	0.1	0.993	2.3576	13.4		62476

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	2.058	2.303	65.2		3.255	3.384	0.92	0.54	1.6	13.4

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	THROUGHOUT	2.06	19.89	62471	3150	68.404	0.182	0.1788	0.1795	0.2342	0.2379	RANDOM	39.025

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]
-0.008			-0.008		0.016

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.041
r_dihedral_angle_3_deg	14.631
r_dihedral_angle_2_deg	11.644
r_dihedral_angle_1_deg	7.47
r_lrange_it	5.698
r_lrange_other	5.693
r_scangle_it	4.146
r_scangle_other	4.145
r_mcangle_it	3.371
r_mcangle_other	3.371
r_scbond_it	2.68
r_scbond_other	2.68
r_mcbond_it	2.2
r_mcbond_other	2.192
r_angle_refined_deg	1.904
r_dihedral_angle_other_2_deg	1.486
r_angle_other_deg	0.738
r_nbd_refined	0.195
r_nbtor_refined	0.165
r_symmetry_xyhbond_nbd_refined	0.156
r_symmetry_nbd_other	0.155
r_xyhbond_nbd_refined	0.136
r_symmetry_nbd_refined	0.133
r_ncsr_local_group_1	0.113
r_nbd_other	0.103
r_ncsr_local_group_2	0.096
r_chiral_restr	0.093
r_ncsr_local_group_3	0.08
r_symmetry_nbtor_other	0.073
r_symmetry_xyhbond_nbd_other	0.059
r_bond_refined_d	0.01
r_gen_planes_refined	0.008
r_gen_planes_other	0.003
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10063
Nucleic Acid Atoms
Solvent Atoms	403
Heterogen Atoms	360

Software

Software
Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
STARANISO	data scaling
XDS	data scaling
MOLREP	phasing