1SY3 | pdb_00001sy3

1.00 A Crystal Structure of D30N Mutant of Nitrophorin 4 from Rhodnius Prolixus 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	37.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.431	α = 90
b = 42.729	β = 94.27
c = 53.124	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 4	Bent conical Si-mirror (Rh coating)	2002-12-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 14-BM-C	0.900	APS	14-BM-C

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	10.6	95	0.073	0.073	17.2	5.12	85604	85604			3.398

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	1.02	99.1		0.124	0.124	3.5	3.06	8863

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	9.68	85604	75616	4005	93.85	0.14281	0.14281	0.14193	0.15	0.15924	0.15	RANDOM	7.253

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]
		0.02	0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	7.389
r_sphericity_free	3.724
r_scangle_it	3.019
r_sphericity_bonded	2.937
r_scbond_it	2.134
r_angle_other_deg	2.1
r_mcangle_it	2
r_angle_refined_deg	1.699
r_mcbond_it	1.327
r_rigid_bond_restr	1.098
r_nbd_other	0.256
r_nbd_refined	0.226
r_symmetry_vdw_other	0.223
r_metal_ion_refined	0.216
r_symmetry_vdw_refined	0.167
r_symmetry_hbond_refined	0.13
r_xyhbond_nbd_refined	0.119
r_chiral_restr	0.103
r_nbtor_other	0.088
r_bond_refined_d	0.012
r_gen_planes_refined	0.009
r_bond_other_d	0.002
r_gen_planes_other	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	1535
Nucleic Acid Atoms
Solvent Atoms	319
Heterogen Atoms	50

Software

Software
Software Name	Purpose
REFMAC	refinement
XDISPLAYF	data reduction
d*TREK	data scaling