9F65 | pdb_00009f65

X-RAY DIFFRACTION

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	9F5V	Crystal structure of thiol peroxidase from Helicobacter pylori (HpTx, reduced)

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	0.1 M BISTRIS, 28% PEG 2000MM

Crystal Properties
Matthews coefficient	Solvent content
2.1	41.29

Symmetry
Space Group	P 1 21 1

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 EIGER2 S 9M		2023-07-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID30B	0.87313	ESRF	ID30B

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.95	30	96.2	0.043	11.8	2.9		24146

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.95	2.05	96.7		0.638	2.1	2.9

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 (Observed)	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	1.95	30	22932	1207	96.16	0.17903	0.17709	0.1828	0.21651	0.2229	RANDOM	55.3

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]
-5.32		2.12	2.88		1.71

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.229
r_dihedral_angle_4_deg	23.016
r_dihedral_angle_3_deg	13.667
r_dihedral_angle_1_deg	6.3
r_long_range_B_other	5.437
r_long_range_B_refined	5.421
r_mcangle_other	4.57
r_mcangle_it	4.563
r_scangle_other	4.446
r_mcbond_it	3.466

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.229
r_dihedral_angle_4_deg	23.016
r_dihedral_angle_3_deg	13.667
r_dihedral_angle_1_deg	6.3
r_long_range_B_other	5.437
r_long_range_B_refined	5.421
r_mcangle_other	4.57
r_mcangle_it	4.563
r_scangle_other	4.446
r_mcbond_it	3.466
r_mcbond_other	3.455
r_scbond_it	3.396
r_scbond_other	3.382
r_angle_refined_deg	1.241
r_angle_other_deg	1.136
r_rigid_bond_restr	0.963
r_chiral_restr	0.048
r_bond_refined_d	0.004
r_gen_planes_refined	0.004
r_gen_planes_other	0.002
r_bond_other_d	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_sphericity_free
r_sphericity_bonded