3P7Y

Pentaerythritol tetranitrate reductase co-crystal structure with bound (E)-1-(2'-hydroxyphenyl)-2-nitroethene

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6.2	293	100mM sodium cacodylate, 100 mM sodium acetate, 16-18% isopropanol, pH 6.2, vapor diffusion, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.28	45.97

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.533	α = 90
b = 70.349	β = 90
c = 88.948	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	ADSC QUANTUM 1		2010-03-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4	1.07	ESRF	ID14-4

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	1.2	55.216	99.5	0.098	0.098	12.2	4.4	112611	112611

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.2	1.26	100		0.274	0.274	2.6	4.5	16325

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1H50	1.2	30.02	112529	5645	99.39	0.126	0.1248	0.1475	RANDOM	9.8403

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]
0.01			0.03		-0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.889
r_dihedral_angle_4_deg	12.592
r_dihedral_angle_3_deg	11.865
r_dihedral_angle_1_deg	5.896
r_sphericity_free	4.054
r_scangle_it	2.448
r_scbond_it	1.821
r_sphericity_bonded	1.786
r_angle_refined_deg	1.364
r_mcangle_it	1.286
r_mcbond_it	0.989
r_angle_other_deg	0.944
r_rigid_bond_restr	0.849
r_mcbond_other	0.362
r_symmetry_vdw_other	0.296
r_symmetry_vdw_refined	0.249
r_symmetry_hbond_refined	0.223
r_nbd_refined	0.212
r_nbd_other	0.209
r_nbtor_refined	0.176
r_xyhbond_nbd_refined	0.112
r_nbtor_other	0.084
r_chiral_restr	0.08
r_bond_refined_d	0.008
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2765
Nucleic Acid Atoms
Solvent Atoms	745
Heterogen Atoms	43

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection