1H50

Structure of Pentaerythritol Tetranitrate Reductase and complexes

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.2		25% PEG 3000, 0.1M SODIUM ACETATE, 0.1M SODIUM CACODYLATE, 17% ISOPROPANOL PH 6.2

Crystal Properties
Matthews coefficient	Solvent content
2.3	38

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.501	α = 90
b = 68.492	β = 90
c = 88.272	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	IMAGE PLATE	RIGAKU RAXIS IV IMAGE PLATE	MIRRORS		M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200

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	91.7	0.045	30.1	3.1		51016			15.9

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				0.12

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	PDB ENTRY 1OYA	1.5	50	50462	2448	90.6	0.193	0.193	0.225	RANDOM	15.5

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]
-1.71			2.94		-1.24

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	23.4
c_angle_deg	1.3
c_improper_angle_d	0.87
c_scangle_it	0.85
c_mcangle_it	0.68
c_scbond_it	0.54
c_mcbond_it	0.38
c_bond_d	0.006
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2779
Nucleic Acid Atoms
Solvent Atoms	500
Heterogen Atoms	35

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
ARP/wARP	phasing
CNS	refinement