4K8J | pdb_00004k8j

Crystal Structure of Staphylococcal nuclease mutant V23L/V66I

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	277	25mM Sodium Phosphate, 35-60% MPD, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.4	48.76

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.2	α = 90
b = 48.2	β = 90
c = 63.8	γ = 90

Symmetry
Space Group	P 41

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	293	CCD	RIGAKU SATURN 92			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.5418

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	1.59	23.29		0.051		2.2		15671		3

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	1.59	1.65			0.747	0.4	1.08	1935

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2	22.55	9238	470	97.9	0.20331	0.20088	0.2037	0.25108	0.2466	RANDOM	46.498

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]
0.09			0.09		-0.18

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.697
r_dihedral_angle_3_deg	18.476
r_dihedral_angle_4_deg	13.691
r_dihedral_angle_1_deg	6.287
r_scangle_it	5.94
r_scbond_it	3.845
r_mcangle_it	2.578
r_angle_refined_deg	2.012
r_mcbond_it	1.598
r_symmetry_hbond_refined	0.364
r_nbtor_refined	0.305
r_nbd_refined	0.227
r_symmetry_vdw_refined	0.21
r_xyhbond_nbd_refined	0.185
r_chiral_restr	0.166
r_bond_refined_d	0.023
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1084
Nucleic Acid Atoms
Solvent Atoms	45
Heterogen Atoms

Software

Software
Software Name	Purpose
CrystalClear	data collection
CCP4	model building
REFMAC	refinement
d*TREK	data reduction
d*TREK	data scaling
CCP4	phasing