7P1F | pdb_00007p1f

Structure of KDNase from Aspergillus terrerus in complex with 2,3-didehydro-2,3-dideoxy-D-glycero-D-galacto-nonulosonic acid.

X-RAY DIFFRACTION

Starting Model(s)

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

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
2.27	45.82

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.318	α = 90
b = 66.833	β = 90.76
c = 92.813	γ = 90

Symmetry
Space Group	P 1 2 1

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-F		2018-12-16	M	SINGLE WAVELENGTH

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

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.29	92.8	96.3	0.059	0.996	7.6	2.6		129965

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.29	1.31	86.6		0.68	0.479

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2xzk	1.45	92.8	123439	6481	97.83	0.1544	0.1521	0.16	0.1986	0.21	RANDOM	17.116

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]
0.22		-0.57	-1.08		0.88

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.14
r_sphericity_free	28.679
r_sphericity_bonded	14.726
r_dihedral_angle_4_deg	13.495
r_dihedral_angle_3_deg	11.301
r_dihedral_angle_1_deg	6.807
r_rigid_bond_restr	4.943
r_angle_refined_deg	1.411
r_angle_other_deg	0.735
r_chiral_restr	0.079

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.14
r_sphericity_free	28.679
r_sphericity_bonded	14.726
r_dihedral_angle_4_deg	13.495
r_dihedral_angle_3_deg	11.301
r_dihedral_angle_1_deg	6.807
r_rigid_bond_restr	4.943
r_angle_refined_deg	1.411
r_angle_other_deg	0.735
r_chiral_restr	0.079
r_bond_refined_d	0.009
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5906
Nucleic Acid Atoms
Solvent Atoms	874
Heterogen Atoms	66

Software

Software
Software Name	Purpose
REFMAC	refinement
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.