7S14 | pdb_00007s14

Crystal structure of putative NAD(P)H-flavin oxidoreductase from Haemophilus influenzae 86-028NP

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	289	0.2 M calcium chloride, 20% w/v PEG3350

Crystal Properties
Matthews coefficient	Solvent content
2.05	40.14

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.833	α = 90
b = 54.779	β = 90.04
c = 134.446	γ = 90

Symmetry
Space Group	P 1 21 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 X 6M		2020-04-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97918	APS	19-ID

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	1.65	50	98.9	0.105	0.992	11.9	4.4		97736

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	1.65	1.68	96.4		0.931	0.453	0.98	3.9

Refinement

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	SAD	THROUGHOUT	1.65	42.47	91789	5030	97.6	0.154	0.152	0.16	0.1914	0.19	RANDOM	29.314

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]
-5.91		-1.42	2.21		3.7

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.034
r_dihedral_angle_3_deg	15.26
r_dihedral_angle_4_deg	15.036
r_dihedral_angle_1_deg	5.919
r_angle_other_deg	1.18
r_angle_refined_deg	1.176
r_rigid_bond_restr	1.14
r_chiral_restr	0.05
r_gen_planes_other	0.011
r_gen_planes_refined	0.007

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.034
r_dihedral_angle_3_deg	15.26
r_dihedral_angle_4_deg	15.036
r_dihedral_angle_1_deg	5.919
r_angle_other_deg	1.18
r_angle_refined_deg	1.176
r_rigid_bond_restr	1.14
r_chiral_restr	0.05
r_gen_planes_other	0.011
r_gen_planes_refined	0.007
r_bond_refined_d	0.003
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7076
Nucleic Acid Atoms
Solvent Atoms	358
Heterogen Atoms	147

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-3000	data scaling
HKL-3000	data reduction
HKL-3000	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.