3ERQ | pdb_00003erq

Crystal structure of Staphylococcal nuclease variant L25K at cryogenic temperature

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	277	22% MPD, 25 mM Potassium Phosphate, Calcium Chloride, pdTp, Soaked in higher % MPD before freezing, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.19	43.82

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 30.978	α = 90
b = 60.282	β = 93.43
c = 37.961	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	BRUKER APEX II	multi-layer optics	2008-06-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SEALED TUBE	OTHER	1.5418

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	2.1	60.28	100	0.0816	0.0349	20.06	15.45	8220	8216			38.6

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	2.1	2.2	100		0.388	0.2114	4.49	11.86	1058

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.1	23.29	8181	8181	803	99.78	0.215	0.215	0.209	0.21	0.278	0.28	RANDOM	31.224

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]
-0.05		0.01	0.01		0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.39
r_dihedral_angle_3_deg	17.072
r_dihedral_angle_4_deg	14.772
r_dihedral_angle_1_deg	7.064
r_scangle_it	3.985
r_scbond_it	2.636
r_mcangle_it	1.683
r_angle_refined_deg	1.216
r_mcbond_it	0.934
r_chiral_restr	0.095

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.39
r_dihedral_angle_3_deg	17.072
r_dihedral_angle_4_deg	14.772
r_dihedral_angle_1_deg	7.064
r_scangle_it	3.985
r_scbond_it	2.636
r_mcangle_it	1.683
r_angle_refined_deg	1.216
r_mcbond_it	0.934
r_chiral_restr	0.095
r_bond_refined_d	0.008
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1034
Nucleic Acid Atoms
Solvent Atoms	45
Heterogen Atoms	26

Software

Software
Software Name	Purpose
SAINT	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
APEX	data collection
SAINT	data reduction

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729.