1PM1

Crystal structure of nitrophorin 2 L122V/L132V mutant complex with imidazole

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1EUO	PDB entry 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
2.08	40.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 39.31	α = 90
b = 125.47	β = 90
c = 33.88	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 4	bent Si-mirror	2003-04-15	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 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	1.1	28.7	91	0.077	0.089	9.3	3.8	62884	62884			8.4

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)
	1.1	1.14	81.2		0.27	0.27	1	3.1	5509

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 1EUO	1.1	28.64	62884	58988	3164	89.94	0.1547	0.1547	0.1536	0.177	RANDOM	10.562

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]
0.56			-0.43		-0.13

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.982
r_sphericity_free	6.979
r_scangle_it	4.479
r_sphericity_bonded	4.297
r_scbond_it	3.184
r_mcangle_it	2.611
r_angle_other_deg	2.021
r_rigid_bond_restr	1.945
r_angle_refined_deg	1.936
r_mcbond_it	1.871
r_nbd_other	0.266
r_symmetry_vdw_other	0.243
r_nbd_refined	0.215
r_symmetry_vdw_refined	0.191
r_symmetry_hbond_refined	0.191
r_chiral_restr	0.157
r_xyhbond_nbd_refined	0.152
r_nbtor_other	0.103
r_bond_refined_d	0.022
r_gen_planes_refined	0.012
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1419
Nucleic Acid Atoms
Solvent Atoms	244
Heterogen Atoms	48

Software

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