5C5M | pdb_00005c5m

Crystal structure of Staphylococcal nuclease variant Delta+PHS T62D / V104E at cryogenic temperature

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3BDC	PDB entry 3BDC

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	277	25% MPD, 25 mM potassium phosphate, calcium chloride, pdTp

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 30.959	α = 90
b = 60.396	β = 94
c = 38.232	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	multi-layer optics	2013-12-01	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	1.7	50	99.9	0.0184	35.25	12.27	15523	15523			27

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	1.7	1.72	100		0.1736		5.72

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 3BDC	1.7	38.14	14686	772	99.63	0.1733	0.1712	0.18	0.2127	0.22	RANDOM	23.384

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]
-1.1		0.46	-0.85		1.87

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.939
r_dihedral_angle_3_deg	14.573
r_dihedral_angle_4_deg	7.982
r_dihedral_angle_1_deg	6.073
r_mcangle_it	1.924
r_angle_refined_deg	1.815
r_mcbond_it	1.372
r_mcbond_other	1.358
r_angle_other_deg	0.829
r_chiral_restr	0.124

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.939
r_dihedral_angle_3_deg	14.573
r_dihedral_angle_4_deg	7.982
r_dihedral_angle_1_deg	6.073
r_mcangle_it	1.924
r_angle_refined_deg	1.815
r_mcbond_it	1.372
r_mcbond_other	1.358
r_angle_other_deg	0.829
r_chiral_restr	0.124
r_bond_refined_d	0.016
r_gen_planes_refined	0.01
r_bond_other_d	0.005
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1036
Nucleic Acid Atoms
Solvent Atoms	127
Heterogen Atoms	26

Software

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