6KRP

Peroxiredoxin from Aeropyrum pernix K1 (ApPrx) 0Cys W88A mutant

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2E2G

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	0.1 M Sodium citrate tribasic dihydrate pH 5.6, 1.0 M Ammonium phosphate monobasic

Crystal Properties
Matthews coefficient	Solvent content
2.73	54.92

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 76.24	α = 105.779
b = 103.285	β = 105.245
c = 105.129	γ = 92.446

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)	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	1.89	50	97.4	0.063	12.3	3.2		230604

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	1.89	1.92			0.465	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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2E2G	1.89	49.368	230599	11796	97.424	0.165	0.1639	0.1883	28.694

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]
0.223	-0.808	1.136	-1.648	-0.953	1.055

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.054
r_dihedral_angle_4_deg	21.043
r_dihedral_angle_3_deg	16.61
r_lrange_it	8.148
r_lrange_other	8.116
r_dihedral_angle_1_deg	6.926
r_scangle_it	5.924
r_scangle_other	5.924
r_scbond_it	3.975
r_scbond_other	3.972
r_mcangle_it	3.685
r_mcangle_other	3.685
r_mcbond_it	2.628
r_mcbond_other	2.627
r_angle_refined_deg	1.757
r_angle_other_deg	1.392
r_symmetry_xyhbond_nbd_refined	0.407
r_xyhbond_nbd_other	0.316
r_symmetry_nbd_refined	0.278
r_nbd_other	0.249
r_xyhbond_nbd_refined	0.216
r_nbd_refined	0.211
r_symmetry_nbd_other	0.199
r_nbtor_refined	0.168
r_symmetry_xyhbond_nbd_other	0.116
r_symmetry_nbtor_other	0.097
r_chiral_restr	0.089
r_bond_refined_d	0.012
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	19622
Nucleic Acid Atoms
Solvent Atoms	1633
Heterogen Atoms	130

Software

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