2GTF

Crystal structure of nitrophorin 2 complex with pyrimidine

X-RAY DIFFRACTION

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Starting Model(s)

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

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
1.88	34.62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 34.374	α = 90
b = 34.374	β = 90
c = 255.82	γ = 90

Symmetry
Space Group	P 41 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	2005-11-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 14-BM-C	0.9	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	23.4	91	0.08	32	5	29002	29002			16

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	73		0.68	2	4	4255

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 1PEE	1.4	23.4	27530	27530	1472	90.98	0.1714	0.1714	0.16934	0.21058	RANDOM	14.402

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]
-0.4			-0.4		0.8

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.126
r_dihedral_angle_3_deg	14.189
r_sphericity_free	10.185
r_dihedral_angle_1_deg	7.189
r_scangle_it	4.814
r_sphericity_bonded	4.285
r_scbond_it	3.797
r_mcangle_it	2.927
r_mcbond_it	2.342
r_rigid_bond_restr	2.002
r_angle_refined_deg	1.895
r_dihedral_angle_4_deg	1.608
r_angle_other_deg	1.527
r_mcbond_other	0.847
r_nbd_refined	0.208
r_symmetry_vdw_other	0.205
r_nbd_other	0.197
r_symmetry_hbond_refined	0.193
r_nbtor_refined	0.183
r_xyhbond_nbd_refined	0.167
r_symmetry_vdw_refined	0.166
r_chiral_restr	0.118
r_nbtor_other	0.093
r_bond_refined_d	0.021
r_gen_planes_refined	0.01
r_bond_other_d	0.004
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1442
Nucleic Acid Atoms
Solvent Atoms	160
Heterogen Atoms	49

Software

Software
Software Name	Purpose
REFMAC	refinement
XDISPLAYF	data reduction
HKL-2000	data scaling