4PNY | pdb_00004pny

Crystal structure of Staphylococcal nuclease variant Delta+PHS I72H 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	8	277	20% MPD, 25 mM potassium phosphate, calcium chloride, pdTp, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 31.172	α = 90
b = 60.573	β = 93.79
c = 37.442	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	multi-layer optics	2013-06-22	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	1.68	50	99.9	0.0301	20.59	8	15921	15921			25.2

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	1.68	1.71	100		0.2093	4.35	5.21	557

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	PDB ENTRY 3BDC	1.68	31.8	15882	15882	791	99.82	0.1975	0.1975	0.1954	0.2037	0.2417	0.2492	RANDOM	23.54

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]
-0.06		0.16	-0.94		0.98

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.101
r_dihedral_angle_3_deg	15.368
r_dihedral_angle_4_deg	9.456
r_dihedral_angle_1_deg	6.6
r_angle_refined_deg	1.904
r_angle_other_deg	0.842
r_chiral_restr	0.122
r_bond_refined_d	0.016
r_gen_planes_refined	0.012
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1044
Nucleic Acid Atoms
Solvent Atoms	86
Heterogen Atoms	26

Software

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