2ASN

Crystal structure of D1A mutant of nitrophorin 2 complexed with imidazole

X-RAY DIFFRACTION

---

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
1.91	35.47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 34.389	α = 90
b = 34.389	β = 90
c = 256.725	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	IMAGE PLATE	MAR scanner 345 mm plate	bent Si-mirror	2003-07-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 14-ID-B	1.1808	APS	14-ID-B

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	1.7	16.3	73.2	0.05	8.9	3	13482	13482			18.7

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)
	1.7	1.79	38		0.138	4.7	2	544

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	1.7	16.3	13482	12802	680	73.89	0.1549	0.1549	0.15209	0.20925	RANDOM	10.071

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			-0.08		0.16

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.308
r_dihedral_angle_3_deg	13.634
r_dihedral_angle_4_deg	8.058
r_dihedral_angle_1_deg	7.103
r_scangle_it	3.711
r_scbond_it	2.979
r_mcangle_it	1.862
r_angle_refined_deg	1.782
r_mcbond_it	1.641
r_angle_other_deg	0.862
r_mcbond_other	0.294
r_nbd_refined	0.193
r_nbd_other	0.191
r_symmetry_vdw_other	0.186
r_nbtor_refined	0.178
r_xyhbond_nbd_refined	0.16
r_symmetry_hbond_refined	0.159
r_symmetry_vdw_refined	0.156
r_chiral_restr	0.108
r_nbtor_other	0.09
r_bond_refined_d	0.019
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1419
Nucleic Acid Atoms
Solvent Atoms	163
Heterogen Atoms	48

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling