3P8J

Y351S mutant of pentaerythritol tetranitrate reductase containing a bound acetate molecule

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1H50

Crystallization

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

Crystal Properties
Matthews coefficient	Solvent content
2.28	46.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.49	α = 90
b = 70.309	β = 90
c = 88.971	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		2008-04-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4	0.970	ESRF	ID14-4

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	29.99	93.6	0.051	14.9	3.62		181871

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	1.04	85.4		0.192	3.9	1.82	16399

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	17.8	181855	9174	93.62	0.1347	0.1341	0.1476	RANDOM	9.8627

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					0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.159
r_dihedral_angle_4_deg	12.899
r_dihedral_angle_3_deg	12.156
r_dihedral_angle_1_deg	5.93
r_sphericity_free	3.589
r_scangle_it	2.234
r_sphericity_bonded	1.923
r_scbond_it	1.641
r_angle_refined_deg	1.406
r_mcangle_it	1.23
r_angle_other_deg	0.93
r_mcbond_it	0.914
r_rigid_bond_restr	0.738
r_nbd_refined	0.517
r_mcbond_other	0.32
r_symmetry_vdw_other	0.295
r_symmetry_vdw_refined	0.262
r_nbd_other	0.259
r_symmetry_hbond_refined	0.192
r_xyhbond_nbd_refined	0.19
r_nbtor_refined	0.182
r_chiral_restr	0.121
r_nbtor_other	0.112
r_gen_planes_refined	0.01
r_bond_refined_d	0.009
r_bond_other_d	0.004
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2759
Nucleic Acid Atoms
Solvent Atoms	768
Heterogen Atoms	35

Software

Software
Software Name	Purpose
d*TREK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
d*TREK	data reduction