8QQ9 | pdb_00008qq9

human carbonic anhydrase I in complex with 1-benzyl-3-(1-hydroxy-3,4-dihydro-1H-benzo[c][1,2]oxaborinin-7-yl)thiourea

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1JV0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	9	296	28-31% PEG4000, 0.2 M Sodium acetate, 0.1 M Tris pH 9.0

Crystal Properties
Matthews coefficient	Solvent content
2.29	46.35

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.878	α = 90
b = 69.835	β = 90
c = 120.735	γ = 90

Symmetry
Space Group	P 21 21 21

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 EIGER2 X 9M		2023-04-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID30B	0.8731	ESRF	ID30B

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	2	43.616	99.9	0.069	0.074	0.999	20.6	13.2		36671

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	2	2.05	99.7		0.488	0.527	0.954	5.3	13.6

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	NONE	2	43.616	36617	1824	99.855	0.205	0.2025	0.2098	0.2555	0.2631	36.399

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]
-1.791			2.861		-1.071

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.362
r_dihedral_angle_4_deg	17.948
r_dihedral_angle_3_deg	14.803
r_dihedral_angle_1_deg	8.129
r_lrange_it	6.441
r_lrange_other	6.441
r_scangle_it	4.889
r_scangle_other	4.888
r_mcangle_it	3.996
r_mcangle_other	3.996
r_scbond_it	3.325
r_scbond_other	3.324
r_mcbond_it	3.048
r_mcbond_other	3.036
r_angle_refined_deg	1.583
r_angle_other_deg	1.297
r_nbd_other	0.208
r_symmetry_xyhbond_nbd_refined	0.207
r_nbd_refined	0.196
r_symmetry_nbd_other	0.187
r_symmetry_nbd_refined	0.187
r_nbtor_refined	0.166
r_xyhbond_nbd_refined	0.138
r_metal_ion_refined	0.087
r_symmetry_nbtor_other	0.079
r_chiral_restr	0.072
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4028
Nucleic Acid Atoms
Solvent Atoms	98
Heterogen Atoms	48

Software

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