3M1J

The crystal structure of a NAMI A-Carbonic Anhydrase II adduct discloses the mode of action of this novel anticancer metallodrug

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.8	277	Tris-HCl pH 7.7-7.8, sodium 4-(hydroxymercury)benzoate, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.09	41.14

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.1	α = 90
b = 41.55	β = 104.51
c = 72.29	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	OXFORD SAPPHIRE CCD		2009-09-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SEALED TUBE	OXFORD DIFFRACTION ENHANCE ULTRA	1.54

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	1.8	10.9	83	0.17	15.7	2.9	42492	35616	2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.8	1.84			0.41	2.38	1.8	7082

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	PDB ENTRY 1CA2	1.8	10.87	21463	1100	100	0.19512	0.19307	0.23549	RANDOM	13.283

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]
		-0.01			-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.715
r_dihedral_angle_4_deg	15.949
r_dihedral_angle_3_deg	15.618
r_dihedral_angle_1_deg	5.8
r_scangle_it	2.099
r_scbond_it	1.294
r_angle_refined_deg	1.162
r_mcangle_it	0.89
r_mcbond_it	0.509
r_nbtor_refined	0.306

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.715
r_dihedral_angle_4_deg	15.949
r_dihedral_angle_3_deg	15.618
r_dihedral_angle_1_deg	5.8
r_scangle_it	2.099
r_scbond_it	1.294
r_angle_refined_deg	1.162
r_mcangle_it	0.89
r_mcbond_it	0.509
r_nbtor_refined	0.306
r_nbd_refined	0.194
r_symmetry_vdw_refined	0.162
r_symmetry_hbond_refined	0.116
r_xyhbond_nbd_refined	0.112
r_chiral_restr	0.081
r_metal_ion_refined	0.039
r_bond_refined_d	0.008
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2048
Nucleic Acid Atoms
Solvent Atoms	188
Heterogen Atoms	21

Software

Software
Software Name	Purpose
CrysalisPro	data collection
AMoRE	phasing
REFMAC	refinement
CrysalisPro	data reduction
SCALEPACK	data scaling

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.