8QKZ

Human Carbonic Anhydrase II in complex with 3,4-dihydro-1H-benzo[c][1,2]oxaborinin-1-ol at pH 9.0

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4FIK

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	9	296	1.5 M sodium citrate, 50 mM Tris pH pH 9.0

Crystal Properties
Matthews coefficient	Solvent content
2.11	41.78

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.4	α = 90
b = 41.58	β = 104.56
c = 72.53	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		2021-12-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ELETTRA BEAMLINE 11.2C	1.0	ELETTRA	11.2C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.34	41.072	97.7	0.069	0.074	0.996	12.7	6.1		53818

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.34	1.36	94.8		0.211	0.236	0.959	4.4	5.2

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 (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	NONE	1.34	41.072	53788	2681	97.704	0.115	0.1127	0.1513	14.142

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]
-0.326		0.298	-0.233		0.356

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.844
r_dihedral_angle_4_deg	24.402
r_dihedral_angle_3_deg	12.002
r_rigid_bond_restr	7.535
r_dihedral_angle_1_deg	6.936
r_lrange_it	4.498
r_scangle_it	4.473
r_scangle_other	4.472
r_lrange_other	4.463
r_scbond_it	3.771
r_scbond_other	3.769
r_mcangle_other	2.866
r_mcangle_it	2.865
r_mcbond_it	2.42
r_mcbond_other	2.419
r_angle_refined_deg	2.208
r_angle_other_deg	1.553
r_symmetry_nbd_refined	0.276
r_nbd_other	0.236
r_nbd_refined	0.235
r_symmetry_nbd_other	0.203
r_nbtor_refined	0.179
r_symmetry_xyhbond_nbd_refined	0.145
r_chiral_restr	0.128
r_xyhbond_nbd_refined	0.118
r_symmetry_nbtor_other	0.094
r_metal_ion_refined	0.049
r_bond_refined_d	0.018
r_gen_planes_refined	0.012
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2045
Nucleic Acid Atoms
Solvent Atoms	271
Heterogen Atoms	17

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
REFMAC	phasing