1SY1 | pdb_00001sy1

1.0 A Crystal Structure of T121V Mutant of Nitrophorin 4 Complexed with Nitric Oxide

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.6	298	Ammonium Phosphate 3.2 M, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
1.96	37.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.395	α = 90
b = 42.724	β = 94.31
c = 53.032	γ = 90

Symmetry
Space Group	C 1 2 1

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 315	Flat mirror (vertical focusing)	2002-02-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-1	0.751	SSRL	BL9-1

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	1.01	30.6	96.1	0.043	0.043	16.6	3.66	80037	80037			3.96

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)
	1.01	1.04	88.6		0.175	0.175	6.2	3.46	7313

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 1KOI	1.01	26.44	80037	75071	3967	96.06	0.13006	0.13006	0.1293	0.13	0.14452	0.13	RANDOM	6.09

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	-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	7.45
r_sphericity_free	4.162
r_scangle_it	3.088
r_sphericity_bonded	2.734
r_angle_other_deg	2.576
r_scbond_it	2.137
r_mcangle_it	1.775
r_angle_refined_deg	1.729
r_mcbond_it	1.172
r_rigid_bond_restr	1.093
r_metal_ion_refined	0.38
r_symmetry_vdw_other	0.269
r_nbd_other	0.251
r_nbd_refined	0.236
r_xyhbond_nbd_refined	0.172
r_symmetry_vdw_refined	0.167
r_symmetry_hbond_refined	0.108
r_chiral_restr	0.103
r_nbtor_other	0.089
r_gen_planes_other	0.022
r_gen_planes_refined	0.015
r_bond_refined_d	0.013
r_bond_other_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1448
Nucleic Acid Atoms
Solvent Atoms	265
Heterogen Atoms	50

Software

Software
Software Name	Purpose
REFMAC	refinement
Blu-Ice	data collection
d*TREK	data scaling