3P1H | pdb_00003p1h

Crystal structure of Staphylococcal nuclease variant Delta+PHS V23K/I92A at cryogenic temperature

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3BDC	PDB ID: 3BDC Residues 7-141, deleted waters and cofactors, all B factors set to 20.00 A2, truncated: H8A, T13A, V23A, Q30A, K64A, T82A, I92A, Y113A, V114A, Y115A

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	9	277	27% MPD, 25 mM Potassium Phosphate, Calcium Chloride, pdTp, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.36

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 31.131	α = 90
b = 60.448	β = 93.56
c = 37.972	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	100	CCD	ADSC QUANTUM 315	mirrors	2009-07-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X25	0.97950	NSLS	X25

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	1.79	50	98	0.075	14.7	11.8	13067	13067			31.26

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	1.79	1.82	97		0.28		12.4	649

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 ID: 3BDC Residues 7-141, deleted waters and cofactors, all B factors set to 20.00 A2, truncated: H8A, T13A, V23A, Q30A, K64A, T82A, I92A, Y113A, V114A, Y115A	1.79	22.94	13040	13040	1298	98.06	0.1841	0.1841	0.1791	0.18	0.2307	0.23	RANDOM	24.8326

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]
-1.76		0.37	-1.31		3.12

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.724
r_dihedral_angle_4_deg	18.262
r_dihedral_angle_3_deg	16.062
r_dihedral_angle_1_deg	6.37
r_scangle_it	4.715
r_scbond_it	3.27
r_mcangle_it	1.946
r_angle_refined_deg	1.499
r_mcbond_it	1.252
r_chiral_restr	0.122

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.724
r_dihedral_angle_4_deg	18.262
r_dihedral_angle_3_deg	16.062
r_dihedral_angle_1_deg	6.37
r_scangle_it	4.715
r_scbond_it	3.27
r_mcangle_it	1.946
r_angle_refined_deg	1.499
r_mcbond_it	1.252
r_chiral_restr	0.122
r_bond_refined_d	0.014
r_gen_planes_refined	0.012

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1032
Nucleic Acid Atoms
Solvent Atoms	61
Heterogen Atoms	26

Software

Software
Software Name	Purpose
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-2000	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.