7P1D

Structure of KDNase from Aspergillus Terrerus in complex with 2-keto-3-deoxynononic acid

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2XCY

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	20% PEG 6K, 0.1M MES pH6 , 0.2M Calcium Chloride

Crystal Properties
Matthews coefficient	Solvent content
2.17	43.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.652	α = 90
b = 67.045	β = 90
c = 93.507	γ = 90

Symmetry
Space Group	P 21 2 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	173	PIXEL	DECTRIS PILATUS 6M		2018-12-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9159	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	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	1.69	67.04	98.4	0.99	8.3	5.2		43029

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.69	1.74			0.78

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2xcy	1.69	67.04	40778	2213	98.09	0.2023	0.2003	0.2379	RANDOM	25.455

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]
0.21			-0.71		0.5

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.681
r_dihedral_angle_4_deg	14.733
r_dihedral_angle_3_deg	12.839
r_dihedral_angle_1_deg	6.855
r_angle_refined_deg	1.53
r_angle_other_deg	0.829
r_chiral_restr	0.09
r_bond_refined_d	0.014
r_gen_planes_refined	0.007
r_bond_other_d	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.681
r_dihedral_angle_4_deg	14.733
r_dihedral_angle_3_deg	12.839
r_dihedral_angle_1_deg	6.855
r_angle_refined_deg	1.53
r_angle_other_deg	0.829
r_chiral_restr	0.09
r_bond_refined_d	0.014
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2943
Nucleic Acid Atoms
Solvent Atoms	319
Heterogen Atoms	37

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
xia2	data reduction
xia2	data scaling
PHASER	phasing

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.