1SXU

1.4 A Crystal Structure of D30N Mutant of Nitrophorin 4 from Rhodnius Prolixus Complexed with Imidazole

X-RAY DIFFRACTION

---

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.6	298	PEG 4000, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
1.94	36.69

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.135	α = 90
b = 42.541	β = 94.12
c = 52.995	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	IMAGE PLATE	RIGAKU RAXIS IV		2001-05-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.54

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	1.36	20.4	99.3	0.034	0.034	20.3	2.53	33304	33304			8.93

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)
	1.36	1.41	96.3		0.07	0.07	7.7	1.31	3213

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	1IKJ	1.4	20.4	33304	29297	1539	99.97	0.14264	0.14264	0.14092	0.17534	RANDOM	12.055

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]
-0.08		-0.09	-0.09		0.16

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.862
r_sphericity_free	5.552
r_scangle_it	4.626
r_sphericity_bonded	3.585
r_scbond_it	3.228
r_mcangle_it	2.569
r_angle_refined_deg	1.816
r_mcbond_it	1.67
r_rigid_bond_restr	1.661
r_symmetry_vdw_refined	0.223
r_nbd_refined	0.218
r_xyhbond_nbd_refined	0.133
r_chiral_restr	0.126
r_symmetry_hbond_refined	0.092
r_bond_refined_d	0.018
r_gen_planes_refined	0.011
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_mcbond_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1447
Nucleic Acid Atoms
Solvent Atoms	232
Heterogen Atoms	48

Software

Software
Software Name	Purpose
REFMAC	refinement
d*TREK	data scaling