1SXW | pdb_00001sxw

1.05 A Crystal Structure of D30A 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
1.97	37.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.358	α = 90
b = 42.839	β = 94.14
c = 53.077	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	1.05	21.9	97.9	0.059	0.059	12.3	2.98	71942	71942			6.84

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	1.05	1.09	99.4		0.259	0.259	2.2	2.15	7226

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	1.05	16.24	71942	67153	3571	96.29	0.15354	0.15354	0.15221	0.1568	0.17857	0.1603	RANDOM	8.166

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_sphericity_free	7.423
r_dihedral_angle_1_deg	7.418
r_sphericity_bonded	4.66
r_scangle_it	4.541
r_scbond_it	3.308
r_mcangle_it	2.736
r_mcbond_it	1.975
r_rigid_bond_restr	1.944
r_angle_refined_deg	1.59
r_angle_other_deg	0.727
r_metal_ion_refined	0.311
r_nbd_other	0.278
r_symmetry_vdw_other	0.265
r_nbd_refined	0.249
r_xyhbond_nbd_refined	0.189
r_symmetry_vdw_refined	0.165
r_symmetry_hbond_refined	0.134
r_chiral_restr	0.118
r_nbtor_other	0.09
r_bond_refined_d	0.017
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_gen_planes_other
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	1425
Nucleic Acid Atoms
Solvent Atoms	329
Heterogen Atoms	50

Software

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