1T68 | pdb_00001t68

Crystal structure of nitrophorin 2 complex with NO

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	298	sodium citrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2	39.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 39.295	α = 90
b = 125.444	β = 90
c = 33.196	γ = 90

Symmetry
Space Group	P 21 21 2

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 4	bent Si-mirror	2003-04-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 14-BM-C	0.9000	APS	14-BM-C

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	1.45	22.8	89.3	0.093	13.2	4.4	26809	26809			17.1

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)
	1.45	1.5	98.1		0.246	2.3	4.5	2879

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	FOURIER SYNTHESIS	THROUGHOUT	PDB ENTRY 1EUO	1.45	22.8	25400	25400	1291	88.91	0.19488	0.19488	0.19291	0.2	0.23462	0.19	RANDOM	20.273

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]
-0.22			-0.28		0.5

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	7.605
r_sphericity_free	6.293
r_scangle_it	5.003
r_sphericity_bonded	3.848
r_scbond_it	3.538
r_mcangle_it	2.896
r_angle_refined_deg	1.989
r_rigid_bond_restr	1.967
r_mcbond_it	1.926
r_angle_other_deg	0.89
r_symmetry_vdw_refined	0.348
r_nbd_other	0.266
r_symmetry_vdw_other	0.246
r_nbd_refined	0.198
r_xyhbond_nbd_refined	0.146
r_symmetry_hbond_refined	0.142
r_chiral_restr	0.121
r_nbtor_other	0.091
r_metal_ion_refined	0.062
r_bond_refined_d	0.022
r_gen_planes_refined	0.01
r_bond_other_d	0.005
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1416
Nucleic Acid Atoms
Solvent Atoms	102
Heterogen Atoms	45

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
CCP4	data scaling