Experiment: 3R5Z

Structure of a Deazaflavin-dependent reductase from Nocardia farcinica, with co-factor F420

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3R5Y	PDB entry 3R5Y

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.6	277	30% PEG 2000, 0.1M acetate, 0.2M (NH4)2SO4 with equimolar protein and co-factor, pH 4.6, vapor diffusion, sitting drop, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 39.704	α = 90
b = 56.939	β = 105.52
c = 66.003	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	CCD	ADSC QUANTUM 315r		2009-10-28		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.3	0.976	ALS	5.0.3

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	1.5	50	93.5	0.08	18	2.3	42118	42118

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	1.5	1.55	82.1		0.473	1.559	1.8	3648

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	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	PDB entry 3R5Y	1.503	37.515	0.05	38975	38957	1967	86.2	0.1675	0.1662	0.1698	0.192	0.1915	random	21.3403

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]
5.1172		1.8438	-1.3982		-3.719

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	19.733
f_angle_d	1.49
f_chiral_restr	0.1
f_bond_d	0.013
f_plane_restr	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2236
Nucleic Acid Atoms
Solvent Atoms	241
Heterogen Atoms	111

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
BOS	data collection
HKL-2000	data reduction
HKL-2000	data scaling