9ERU | pdb_00009eru

Mouse CNPase catalytic domain with nanobody 7E

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2XMI
experimental model	PDB	6HJ7	chain C

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4	277	0.1 M MIB pH 4.0, 25% PEG3350

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 37.15	α = 77.675
b = 79	β = 87.706
c = 117.59	γ = 84.29

Symmetry
Space Group	P 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	PIXEL	DECTRIS EIGER X 16M		2021-04-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, DESY BEAMLINE P11	1.033	PETRA III, DESY	P11

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	2.5	50	91.7	0.205	0.992	5.5	3.8		41229			54.93

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	2.5	2.56	91.3		2.914	0.335	0.6	3.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.5	41.96	1.96	41145	1994	91.53	0.2567	0.2545	0.2538	0.3004	0.3008	69.98

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	13.5216
f_angle_d	0.6648
f_chiral_restr	0.0435
f_bond_d	0.0041
f_plane_restr	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10333
Nucleic Acid Atoms
Solvent Atoms	3
Heterogen Atoms

Software

Software
Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	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.