5C5L | pdb_00005c5l

Crystal structure of Staphylococcal nuclease variant Delta+PHS T62E / L125E at cryogenic temperature

X-RAY DIFFRACTION

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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	6	277	35% MPD, 25 mM potassium phosphate, calcium chloride, pdTp

Crystal Properties
Matthews coefficient	Solvent content
1.9	35.13

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 30.709	α = 90
b = 58.135	β = 98.79
c = 34.796	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	2014-08-27	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	1.75	58.13	100	0.0359	22.4	8.11	12299	12299			20.1

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	1.75	1.77	100		0.1902		5.68

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	1.75	34.39	11694	587	99.98	0.1459	0.1436	0.1567	0.1907	0.1926	RANDOM	13.082

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]
-0.17		0.5	-0.14		0.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.341
r_dihedral_angle_3_deg	15.523
r_dihedral_angle_4_deg	7.957
r_dihedral_angle_1_deg	6.03
r_angle_refined_deg	1.908
r_mcangle_it	1.111
r_angle_other_deg	0.907
r_mcbond_it	0.734
r_mcbond_other	0.662
r_chiral_restr	0.119
r_bond_refined_d	0.018
r_gen_planes_refined	0.011
r_gen_planes_other	0.003
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1045
Nucleic Acid Atoms
Solvent Atoms	114
Heterogen Atoms	31

Software

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