7C8A | pdb_00007c8a

Peroxiredoxin from Aeropyrum pernix K1 (ApPrx) C50S/F80C/C207S/C213S mutant modified with 2-(bromoacetyl)naphthalene(Naph@ApPrx*)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6KRK

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	The reservoir solution contained 0.10 M sodium citrate (pH5.5) 0.20 M lithium sulfate 15% (v/v) reagent alcohol.

Crystal Properties
Matthews coefficient	Solvent content
2.65	53.56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 75.999	α = 105.936
b = 103.081	β = 104.945
c = 105.029	γ = 92.381

Symmetry
Space Group	P 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		2019-05-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL26B1	1.0	SPring-8	BL26B1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.1	50	98.1	0.068	0.998	11.8	3.7		169516

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.14			0.535	0.833	2.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	6KRK	2.1	49.244	169364	8444	97.842	0.169	0.1661	0.17	0.2172	0.22	39.142

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]
-0.002	0.004		0.005	0.003	-0.004

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.599
r_dihedral_angle_4_deg	19.593
r_dihedral_angle_3_deg	18.229
r_dihedral_angle_other_3_deg	14.629
r_lrange_it	8.038
r_lrange_other	8.033
r_dihedral_angle_1_deg	6.957
r_scangle_it	6.217
r_scangle_other	6.217
r_scbond_it	4.14
r_scbond_other	4.139
r_mcangle_it	3.988
r_mcangle_other	3.987
r_mcbond_it	2.904
r_mcbond_other	2.903
r_angle_other_deg	2.097
r_angle_refined_deg	1.594
r_symmetry_nbd_refined	0.306
r_symmetry_xyhbond_nbd_refined	0.265
r_nbd_other	0.255
r_nbd_refined	0.204
r_symmetry_nbd_other	0.193
r_nbtor_refined	0.17
r_xyhbond_nbd_refined	0.153
r_symmetry_xyhbond_nbd_other	0.103
r_symmetry_nbtor_other	0.094
r_chiral_restr	0.075
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	19680
Nucleic Acid Atoms
Solvent Atoms	854
Heterogen Atoms	260

Software

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