6YLZ

X-ray structure of the K72I,Y129F,R133L, H199A quadruple mutant of PNP-oxidase from E. coli

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1G76

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	100 mM KPHO pH 7,5, 5 mM 2-mercaptoethanol, 150 mM NaCl

Crystal Properties
Matthews coefficient	Solvent content
2.88	57.26

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.776	α = 90
b = 63.776	β = 90
c = 124.727	γ = 120

Symmetry
Space Group	P 31 2 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 PILATUS3 6M		2020-02-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.968620	Diamond	I24

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	1.558	55.233	98	0.13	0.134	0.03	0.999	13.6	19.7		41877

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.558	1.585	98		0.803	0.444	0.9	11.91

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	FREE R-VALUE	1G76	1.558	55.232	41608	2061	97.351	0.172	0.1706	0.2022	33.06

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]
0.778	0.389		0.778		-2.524

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.336
r_dihedral_angle_3_deg	13.685
r_dihedral_angle_4_deg	13.185
r_lrange_it	8.08
r_lrange_other	7.994
r_dihedral_angle_1_deg	7.082
r_scangle_it	6.075
r_scangle_other	6.061
r_mcangle_other	4.181
r_mcangle_it	4.178
r_scbond_it	4.036
r_scbond_other	3.972
r_mcbond_it	3.017
r_mcbond_other	3.008
r_angle_refined_deg	1.721
r_angle_other_deg	1.428
r_nbd_refined	0.272
r_xyhbond_nbd_refined	0.237
r_symmetry_xyhbond_nbd_refined	0.204
r_symmetry_nbd_other	0.196
r_nbd_other	0.193
r_nbtor_refined	0.175
r_symmetry_nbd_refined	0.173
r_symmetry_nbtor_other	0.084
r_chiral_restr	0.083
r_bond_refined_d	0.013
r_gen_planes_refined	0.012
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1748
Nucleic Acid Atoms
Solvent Atoms	174
Heterogen Atoms	46

Software

Software
Software Name	Purpose
REFMAC	refinement
autoPROC	data collection
autoPROC	data processing
XDS	data reduction
XDS	data scaling
Aimless	data processing
MOLREP	phasing
Coot	model building