7P1Q | pdb_00007p1q

Structure of KDNase from Trichophyton Rubrum 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	2XZJ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	293	25% PEG 1500, 0.1M MMT pH8

Crystal Properties
Matthews coefficient	Solvent content
2.25	45.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.922	α = 90
b = 74.472	β = 90
c = 161.365	γ = 90

Symmetry
Space Group	C 2 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-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)	Rrim I (All)	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	0.91	80.69	84.3	0.048	0.999	14.6	5.2		226869

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	0.91	0.93			0.821	0.534

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	2xzj	0.91	80.68	215570	11219	84.32	0.1411	0.1403	0.15	0.1556	0.17	RANDOM	11

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]
-1.09			0.78		0.31

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.742
r_sphericity_free	23.07
r_dihedral_angle_4_deg	15.303
r_sphericity_bonded	11.401
r_dihedral_angle_3_deg	10.754
r_dihedral_angle_1_deg	7.217
r_rigid_bond_restr	4.817
r_angle_refined_deg	1.565
r_angle_other_deg	0.878
r_chiral_restr	0.101

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.742
r_sphericity_free	23.07
r_dihedral_angle_4_deg	15.303
r_sphericity_bonded	11.401
r_dihedral_angle_3_deg	10.754
r_dihedral_angle_1_deg	7.217
r_rigid_bond_restr	4.817
r_angle_refined_deg	1.565
r_angle_other_deg	0.878
r_chiral_restr	0.101
r_bond_refined_d	0.012
r_gen_planes_refined	0.01
r_bond_other_d	0.003
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2938
Nucleic Acid Atoms
Solvent Atoms	509
Heterogen Atoms	60

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.