3ITP | pdb_00003itp

Crystal structure of Staphylococcal nuclease variant Delta+PHS F34K 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 ID 3BDC, residue 34 truncated to ALA, all water molecules and ligands were removed, All b-factors set to 20A^2, all alternate residue conformations deleted, defaulting to conformation A

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	277	29%(w/v) MPD, 25 mM Potassium Phosphate, Calcium Chloride (3 M eq), pdTp (2 M eq), 5.5 (mg protein)/mL in stock solution; 4uL protein stock and 4uL well solution per drop; 1-2 weeks of growth, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.22	44.52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 31.027	α = 90
b = 60.296	β = 92.26
c = 38.249	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	Meridionally-bent fused silica mirror with palladium and uncoated stripes	2009-08-20	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	1.55	40	93.9	0.046	26.9	7.3	20523	19271

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)
	1.55	1.58	60.1		0.323		3.6	606

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, residue 34 truncated to ALA, all water molecules and ligands were removed, All b-factors set to 20A^2, all alternate residue conformations deleted, defaulting to conformation A	1.75	32.28	14283	14262	749	99.85	0.205	0.204	0.203	0.1999	0.235	0.2338	RANDOM	30.152

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		0.03	-0.04		0.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.138
r_dihedral_angle_3_deg	13.329
r_dihedral_angle_4_deg	12.152
r_scangle_it	6.371
r_dihedral_angle_1_deg	5.36
r_scbond_it	4.062
r_mcangle_it	2.599
r_mcbond_it	1.526
r_angle_refined_deg	1.215
r_chiral_restr	0.121
r_bond_refined_d	0.026
r_gen_planes_refined	0.012

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1031
Nucleic Acid Atoms
Solvent Atoms	72
Heterogen Atoms	26

Software

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