8OO8

Three-Dimensional Structure of Human Carbonic Anhydrase II in Complex with a Covalent Inhibitor

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5AMD

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		294	A 9 0.06 M Divalents 0.1 M Buffer System 3 8.5 30 % v/v Precipitant Mix 1 0.06 M Magnesium chloride hexahydrate; 0.06 M Calcium chloride dihydrate, 0.1 M Tris pH 8.5, 20% v/v PEG 500 MME; 10 % w/v PEG 20000. (Morpheus A-9)

Crystal Properties
Matthews coefficient	Solvent content
2.15	42.73

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.45	α = 90
b = 41.57	β = 104.4
c = 72.79	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	PIXEL	DECTRIS PILATUS 6M		2021-06-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.97625	BESSY	14.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.4	70.5	96.9	0.143	6.5	5		47352			8.9

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.4	1.47	98		0.482	3	5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	1.4	70.5	44917	2410	96.6	0.18614	0.18455	0.21516	RANDOM	11.024

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]
-0.33		-0.19	0.26		0.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	12.437
r_dihedral_angle_2_deg	9.8
r_dihedral_angle_1_deg	7.073
r_long_range_B_refined	4.618
r_long_range_B_other	4.293
r_scangle_other	2.813
r_mcangle_other	1.987
r_mcangle_it	1.986
r_scbond_it	1.865
r_scbond_other	1.865
r_angle_refined_deg	1.667
r_mcbond_it	1.272
r_mcbond_other	1.268
r_angle_other_deg	0.904
r_chiral_restr	0.081
r_gen_planes_other	0.018
r_bond_refined_d	0.016
r_gen_planes_refined	0.011
r_bond_other_d	0.002
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2068
Nucleic Acid Atoms
Solvent Atoms	338
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
SCALA	data scaling