4LTD | pdb_00004ltd

Crystal structures of NADH:FMN oxidoreductase (EMOB) - apo form

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	277	10 mg/mL EmoB in 20 mM sodium acetate, pH 5, 1 mM EDTA, 1 mM DTT mixed with an equal volume of reservoir solution (0.1 M MES, pH 6.5, 1.6 M ammonium sulfate, 10% dioxane), VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
4.51	72.74

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.925	α = 90
b = 100.925	β = 90
c = 129.61	γ = 120

Symmetry
Space Group	P 64 2 2

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	ADSC QUANTUM 315r		2007-12-01	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.1	1.0332, 0.97925, 0.97942, 0.91162	ALS	8.2.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.186	24.241				36423	17012		2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.186

Refinement

Statistics
Diffraction ID	Structure Solution Method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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	MAD	2.186	24.241	4.1	17012	1702	81.88	0.1708	0.1685	0.1709	0.1918	0.191	RANDOM

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	11.744
f_angle_d	1.167
f_chiral_restr	0.08
f_bond_d	0.009
f_plane_restr	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1404
Nucleic Acid Atoms
Solvent Atoms	116
Heterogen Atoms	20

Software

Software
Software Name	Purpose
ADSC	data collection
X-PLOR	model building
PHENIX	refinement
CrystalClear	data reduction
CrystalClear	data scaling
X-PLOR	phasing