5IGD

Crystal structure of Staphylococcal nuclease variant Delta+PHS T62H/I92E at cryogenic temperature

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	9	277	20% MPD, 25 mM potassium phosphate, calcium chloride, pdTp

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 31.122	α = 90
b = 60.38	β = 93.7
c = 38.259	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	110	CCD	APEX II CCD	mirrors	2014-05-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SEALED TUBE	OTHER	1.54

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	1.8	60.38	100	0.0201	33.7	16.29		13194			25.6

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	1.8	1.84	100		0.1372	6.71	10.38

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 3BDC	1.8	38.18	12522	652	99.97	0.1937	0.1915	0.2336	RANDOM	25.397

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]
0.01			0.01		-0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.737
r_dihedral_angle_3_deg	13.773
r_dihedral_angle_4_deg	9.338
r_dihedral_angle_1_deg	6.378
r_mcangle_it	3.131
r_mcbond_it	2.351
r_mcbond_other	2.331
r_angle_refined_deg	1.808
r_angle_other_deg	0.932
r_chiral_restr	0.107

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.737
r_dihedral_angle_3_deg	13.773
r_dihedral_angle_4_deg	9.338
r_dihedral_angle_1_deg	6.378
r_mcangle_it	3.131
r_mcbond_it	2.351
r_mcbond_other	2.331
r_angle_refined_deg	1.808
r_angle_other_deg	0.932
r_chiral_restr	0.107
r_bond_refined_d	0.018
r_gen_planes_refined	0.01
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1037
Nucleic Acid Atoms
Solvent Atoms	75
Heterogen Atoms	26

Software

Software
Software Name	Purpose
XPREP	data reduction
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
APEX 2	data reduction

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.