3P75 | pdb_00003p75

Crystal structure of Staphylococcal nuclease variant Delta+PHS V104D 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 with residue 104 truncated to Ala and all b-factors set to 20 A^2. Only conformation A was selected for residues with multiple conformations.

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	9.5	277	35% MPD(w/v), 25 mM CHES, Calcium Chloride, pdTp, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.35	47.73

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 31	α = 90
b = 60.791	β = 93.45
c = 36.838	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.	2009-09-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X25	1.1	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	1.65	50	94.9	0.071	19.4	7.5	15431	15431			40.5

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)
	1.65	1.68	68.6		0.534		4.4	544

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 with residue 104 truncated to Ala and all b-factors set to 20 A^2. Only conformation A was selected for residues with multiple conformations.	1.9	30.94	10782	10782	535	99.53	0.1893	0.1893	0.1866	0.2	0.2389	0.24	RANDOM	38.78

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]
-0.04		0.05	-0.04		0.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.507
r_dihedral_angle_3_deg	17.193
r_dihedral_angle_4_deg	6.88
r_dihedral_angle_1_deg	6.495
r_scangle_it	5.625
r_scbond_it	3.871
r_mcangle_it	2.08
r_mcbond_it	1.433
r_angle_refined_deg	1.023
r_chiral_restr	0.102
r_gen_planes_refined	0.016
r_bond_refined_d	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1034
Nucleic Acid Atoms
Solvent Atoms	54
Heterogen Atoms	27

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