1SY0

1.15 A Crystal Structure of T121V Mutant of Nitrophorin 4 from Rhodnius Prolixus

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1D2U	PDB entry 1D2U

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	298	Ammonium Phosphate 3.2 M, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
1.95	37.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.3	α = 90
b = 42.763	β = 93.66
c = 52.89	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	1.15	21.37	97.1	0.05	0.05	20.8	3.19	54132	54132			5.78

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)
	1.15	1.19	98.6		0.134	0.134	6	2.51	5460

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	PDB entry 1D2U	1.15	21.37	54132	50570	2727	95.62	0.1428	0.1428	0.14128	0.17179	RANDOM	8.884

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		-0.12	-0.22		0.22

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	7.836
r_sphericity_free	5.273
r_scangle_it	3.648
r_sphericity_bonded	3.241
r_scbond_it	2.612
r_mcangle_it	2.347
r_angle_other_deg	1.868
r_angle_refined_deg	1.829
r_mcbond_it	1.531
r_rigid_bond_restr	1.473
r_nbd_refined	0.346
r_nbd_other	0.253
r_symmetry_vdw_other	0.242
r_symmetry_vdw_refined	0.187
r_xyhbond_nbd_refined	0.122
r_chiral_restr	0.116
r_symmetry_hbond_refined	0.089
r_nbtor_other	0.088
r_bond_refined_d	0.016
r_gen_planes_refined	0.011
r_gen_planes_other	0.004
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1475
Nucleic Acid Atoms
Solvent Atoms	241
Heterogen Atoms	44

Software

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