2A3F

Crystal structure of nitrophorin 2 aqua complex

X-RAY DIFFRACTION

---

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	298	sodium citrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2	39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 39.608	α = 90
b = 125.773	β = 90
c = 33.395	γ = 90

Symmetry
Space Group	P 21 21 2

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	bent Si-mirror	2004-04-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 14-BM-C	0.9000	APS	14-BM-C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.4	26	92	0.09	20	5.5	31128	31128			20.9

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.4	1.45	93		0.25	1.5	3.8	3089

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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	1EUO	1.4	26	29280	1563	91.21	0.1794	0.1794	0.17755	0.21391	RANDOM	21.996

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]
-1.16			0.49		0.66

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.153
r_dihedral_angle_3_deg	16.229
r_sphericity_free	11.53
r_dihedral_angle_1_deg	7.288
r_dihedral_angle_4_deg	6.47
r_sphericity_bonded	5.723
r_scangle_it	5.624
r_scbond_it	4.34
r_mcangle_it	3.236
r_mcbond_it	2.586
r_rigid_bond_restr	2.333
r_angle_refined_deg	1.988
r_angle_other_deg	1.585
r_mcbond_other	1.116
r_symmetry_vdw_other	0.222
r_symmetry_vdw_refined	0.212
r_xyhbond_nbd_refined	0.2
r_nbd_refined	0.198
r_nbd_other	0.19
r_nbtor_refined	0.183
r_chiral_restr	0.132
r_nbtor_other	0.096
r_symmetry_hbond_refined	0.087
r_bond_refined_d	0.022
r_gen_planes_refined	0.014
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1422
Nucleic Acid Atoms
Solvent Atoms	104
Heterogen Atoms	48

Software

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