1X8N | pdb_00001x8n

1.08 A Crystal Structure Of Nitrophorin 4 From Rhodnius Prolixus Complexed With Nitric Oxide at pH 7.4

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.4	300	ammonium phosphate, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 300.0K

Crystal Properties
Matthews coefficient	Solvent content
1.63	24.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.147	α = 90
b = 42.775	β = 94.09
c = 53.042	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)	2002-05-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.9800	SSRL	BL11-1

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	1.08	36	98.4	0.059	0.059	10.4	5.5	66157	66157			10.7

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)
	1.08	1.12	95.1		0.27	0.27	1.8	4.6	6226

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 Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	FREE R	1KOI	1.08	6	65756	65756	3303	98.4	0.136	0.13411	0.1341	0.14	0.1714	RANDOM	14.3

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]

Coordinate Error
Structure Solution Method	Refinement High Resolution	Refinement Low Resolution
60	1341	1766.55

RMS Deviations
Key	Refinement Restraint Deviation
s_from_restr_planes	0.426
s_approx_iso_adps	0.087
s_non_zero_chiral_vol	0.081
s_zero_chiral_vol	0.076
s_similar_adp_cmpnt	0.051
s_angle_d	0.033
s_anti_bump_dis_restr	0.032
s_bond_d	0.013
s_rigid_bond_adp_cmpnt	0.005
s_similar_dist

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1552
Nucleic Acid Atoms
Solvent Atoms	316
Heterogen Atoms	45

Software

Software
Software Name	Purpose
DENZO	data reduction
d*TREK	data reduction
SHELX	model building
SHELXL-97	refinement
CrystalClear	data scaling
SHELX	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.