3PNF | pdb_00003pnf

Structure of rat neuronal nitric oxide synthase heme domain in complex with 6-(((3R,4R)-4-(2-((2,2-Difluoro-2-(2-chlorophenyl)ethyl)amino)ethoxy)pyrrolidin-3-yl)methyl)-4-methylpyridin-2-amine

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1OM4	PDB entry 1OM4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.8	278	20-24% PEG3350, 0.1M MES, 100-140mM ammonium acetate, 5mM GSH, 35uM SDS, pH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 278K

Crystal Properties
Matthews coefficient	Solvent content
2.42	49.14

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.982	α = 90
b = 110.678	β = 90
c = 164.149	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	MARMOSAIC 325 mm CCD	mirrors	2010-02-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	1.000	SSRL	BL9-2

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	1.94	50	99.3	0.052	0.052	27.3	4.1		70592		-3	29.3

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	1.94	1.97	100		0.614	0.614	2.8	4.1

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		THROUGHOUT	PDB entry 1OM4	1.94	39.08	66840	3497	98.99	0.17959	0.17772	0.19	0.21493	0.23	RANDOM	42.118

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]
2.13			-0.11		-2.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.3
r_dihedral_angle_4_deg	19.451
r_dihedral_angle_3_deg	14.748
r_dihedral_angle_1_deg	5.805
r_scangle_it	3.438
r_scbond_it	2.223
r_angle_refined_deg	1.49
r_mcangle_it	1.353
r_mcbond_it	0.746
r_chiral_restr	0.107
r_bond_refined_d	0.015
r_gen_planes_refined	0.008
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6676
Nucleic Acid Atoms
Solvent Atoms	398
Heterogen Atoms	187

Software

Software
Software Name	Purpose
Blu-Ice	data collection
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
REFMAC	phasing