1SXX

1.0 A Crystal Structure of D129A/L130A 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	37.39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.219	α = 90
b = 42.751	β = 94.3
c = 53.055	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)	2002-02-20	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	97.1	0.049	0.049	18.5	4.1	80684	80684			4.92

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	89.2		0.239	0.239	5.2	3.46	7370

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	30.57	80684	76166	4036	96.5	0.14123	0.14123	0.1405	0.14	0.15498	0.14	RANDOM	7.307

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	7.253
r_sphericity_free	4.057
r_scangle_it	3.133
r_sphericity_bonded	2.668
r_scbond_it	2.138
r_angle_other_deg	2.074
r_mcangle_it	1.808
r_angle_refined_deg	1.703
r_mcbond_it	1.209
r_rigid_bond_restr	1.109
r_metal_ion_refined	0.398
r_nbd_refined	0.286
r_symmetry_vdw_other	0.254
r_nbd_other	0.252
r_symmetry_vdw_refined	0.174
r_xyhbond_nbd_refined	0.118
r_chiral_restr	0.105
r_nbtor_other	0.09
r_symmetry_hbond_refined	0.089
r_bond_refined_d	0.012
r_gen_planes_refined	0.008
r_gen_planes_other	0.003
r_bond_other_d	0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_mcbond_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1474
Nucleic Acid Atoms
Solvent Atoms	242
Heterogen Atoms	50

Software

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