3FLL

Crystal structure of E55Q mutant of nitrophorin 4

X-RAY DIFFRACTION

---

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.6	298	ammonium phosphate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
1.97	37.42

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.379	α = 90
b = 42.838	β = 94.2
c = 53.056	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	mirrors	2008-02-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-1	0.751	SSRL	BL9-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.5	30.6	95.58	0.081	10.3	3.17		23089

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.5	1.55	100		0.295	2.7	3.15	2527

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	1D2U	1.5	30	23089	23089	1220	95.58	0.171	0.171	0.16886	0.20123	RANDOM	10.663

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]
-0.04			0.48		-0.45

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.51
r_dihedral_angle_3_deg	13.183
r_dihedral_angle_1_deg	7.084
r_dihedral_angle_4_deg	6.563
r_scangle_it	3.24
r_scbond_it	2.516
r_mcangle_it	1.551
r_angle_refined_deg	1.501
r_angle_other_deg	1.405
r_mcbond_it	1.285
r_mcbond_other	0.241
r_nbd_refined	0.223
r_symmetry_vdw_other	0.203
r_nbd_other	0.19
r_nbtor_refined	0.183
r_xyhbond_nbd_refined	0.158
r_symmetry_vdw_refined	0.115
r_symmetry_hbond_refined	0.114
r_nbtor_other	0.087
r_chiral_restr	0.083
r_bond_refined_d	0.014
r_gen_planes_refined	0.007
r_metal_ion_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1476
Nucleic Acid Atoms
Solvent Atoms	244
Heterogen Atoms	44

Software

Software
Software Name	Purpose
ADSC	data collection
REFMAC	refinement
CrystalClear	data reduction
CrystalClear	data scaling
REFMAC	phasing