3P8I | pdb_00003p8i

Y351F 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
2.19	43.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.685	α = 90
b = 68.838	β = 90
c = 88.915	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	1.19	37.4	99.3	0.077	10.6	3.8	111179	111179

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)
	1.19	1.23	99.7		0.248	4.4

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1H50	1.19	7.98	110924	5564	99.5	0.1302	0.1293	0.13	0.1467	0.14	RANDOM	13.1949

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	40.523
r_dihedral_angle_4_deg	15.308
r_dihedral_angle_3_deg	11.936
r_dihedral_angle_1_deg	5.67
r_sphericity_free	4.571
r_sphericity_bonded	3.488
r_scangle_it	3.012
r_scbond_it	2.118
r_mcangle_it	1.545
r_angle_refined_deg	1.381
r_angle_other_deg	1.379
r_mcbond_it	1.202
r_rigid_bond_restr	1.095
r_mcbond_other	0.867
r_symmetry_vdw_other	0.294
r_symmetry_hbond_refined	0.261
r_symmetry_vdw_refined	0.244
r_nbd_other	0.224
r_nbd_refined	0.211
r_nbtor_refined	0.175
r_xyhbond_nbd_refined	0.128
r_chiral_restr	0.082
r_nbtor_other	0.077
r_bond_refined_d	0.01
r_gen_planes_refined	0.009
r_gen_planes_other	0.003
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2758
Nucleic Acid Atoms
Solvent Atoms	774
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