8BJX | pdb_00008bjx

Crystal structure of human Carbonic anhydrase II in complex with (R)-4-(3-(1-(6-nitropyridin-2-yl)pyrrolidin-3-yl)thioureido)benzenesulfonamide

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	296	1.5 M sodium citrate, 0.1 M Tris pH 8.0

Crystal Properties
Matthews coefficient	Solvent content
2.07	40.45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.32	α = 90
b = 41.17	β = 104.335
c = 71.67	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		2022-03-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ELETTRA BEAMLINE 11.2C	0.999	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	1.28	48	84.1	0.138	0.152	0.984	7.61	5.1		51575

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	1.28	1.32	36.1		0.525	0.617	0.831	2.1	3.38

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	NONE	4FIK	1.283	41.036	51563	2504	84.034	0.158	0.1562	0.17	0.2033	0.21	18.559

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]
-1.934		0.81	-1.312		2.505

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.383
r_dihedral_angle_4_deg	19.859
r_dihedral_angle_3_deg	12.638
r_dihedral_angle_1_deg	7.284
r_rigid_bond_restr	4.221
r_scangle_it	4.14
r_scangle_other	4.139
r_lrange_it	3.981
r_lrange_other	3.98
r_scbond_it	3.764
r_scbond_other	3.764
r_mcangle_other	2.621
r_mcangle_it	2.6
r_mcbond_it	2.406
r_mcbond_other	2.267
r_angle_refined_deg	2.059
r_angle_other_deg	1.525
r_nbd_refined	0.23
r_metal_ion_refined	0.224
r_symmetry_nbd_other	0.207
r_nbd_other	0.205
r_symmetry_nbd_refined	0.192
r_symmetry_xyhbond_nbd_refined	0.192
r_xyhbond_nbd_refined	0.185
r_nbtor_refined	0.18
r_chiral_restr	0.126
r_symmetry_nbtor_other	0.092
r_bond_refined_d	0.021
r_xyhbond_nbd_other	0.018
r_gen_planes_refined	0.014
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2045
Nucleic Acid Atoms
Solvent Atoms	167
Heterogen Atoms	39

Software

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