2CDU

The Crystal Structure of Water-forming NAD(P)H Oxidase from Lactobacillus sanfranciscensis

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1F8W	PDB ENTRY 1F8W

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7		10 MG/ML PROTEIN, 100MM HEPES PH 7.0, 18% W/V PEG 4000, 8% V/V 2-PROPANOL, 20 MM DITHIOTHREITOL

Crystal Properties
Matthews coefficient	Solvent content
2.3	45.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.636	α = 90
b = 92.644	β = 90
c = 163.465	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MARRESEARCH		2004-03-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID		APS	22-ID

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	1.8	46.4	96.1	0.1	29	8.5		81507		2

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	1.8	1.85	73.8		0.49	1.9	4.1

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1F8W	1.8	81.65	77370	4054	96.1	0.18	0.178	0.19	0.223	0.23	RANDOM	24.07

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]
2.09			-0.11		-1.98

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.542
r_scangle_it	3.935
r_scbond_it	2.378
r_angle_refined_deg	1.542
r_mcangle_it	1.492
r_angle_other_deg	0.992
r_mcbond_it	0.81
r_symmetry_vdw_other	0.291
r_symmetry_hbond_refined	0.251
r_nbd_other	0.249
r_nbd_refined	0.229
r_symmetry_vdw_refined	0.194
r_xyhbond_nbd_refined	0.189
r_chiral_restr	0.097
r_nbtor_other	0.088
r_bond_refined_d	0.015
r_gen_planes_refined	0.006
r_gen_planes_other	0.004
r_bond_other_d	0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6937
Nucleic Acid Atoms
Solvent Atoms	708
Heterogen Atoms	160

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	phasing