6YMH | pdb_00006ymh

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

X-RAY DIFFRACTION

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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
2.26	45.65

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.164	α = 90
b = 54.164	β = 90
c = 271.968	γ = 120

Symmetry
Space Group	P 61

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		2019-06-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.96828	Diamond	I24

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.417	46.907	100	0.217	0.048	0.999	11.9	20.1		17206

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	2.417	2.459	100		0.875	0.392	0.9	17.2

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	FREE R-VALUE	1G76	2.417	46.907	17189	800	99.895	0.193	0.1897	0.2	0.2588	0.26	59.324

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]
-1.799	-0.9		-1.799		5.836

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.122
r_dihedral_angle_4_deg	16.91
r_dihedral_angle_3_deg	16.859
r_lrange_it	7.621
r_lrange_other	7.621
r_dihedral_angle_1_deg	6.864
r_scangle_it	5.2
r_scangle_other	5.199
r_mcangle_it	4.814
r_mcangle_other	4.814
r_scbond_it	3.169
r_scbond_other	3.163
r_mcbond_it	3.055
r_mcbond_other	3.053
r_angle_other_deg	2.237
r_angle_refined_deg	1.784
r_nbd_other	0.229
r_symmetry_nbd_other	0.196
r_symmetry_nbd_refined	0.194
r_nbd_refined	0.181
r_nbtor_refined	0.171
r_xyhbond_nbd_refined	0.158
r_symmetry_xyhbond_nbd_refined	0.141
r_chiral_restr	0.115
r_xyhbond_nbd_other	0.084
r_symmetry_nbtor_other	0.078
r_symmetry_xyhbond_nbd_other	0.069
r_bond_other_d	0.034
r_bond_refined_d	0.014
r_gen_planes_other	0.006
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2925
Nucleic Acid Atoms
Solvent Atoms	45
Heterogen Atoms	83

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