9HXZ | pdb_00009hxz

crystal structure of human carbonic anhydrase II in complex with sonepiprazole

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	8	296	1.5 M sodium citrate, 0.1 M Tris pH 8.0

Crystal Properties
Matthews coefficient	Solvent content
2.11	41.57

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.4	α = 90
b = 41.6	β = 104.443
c = 72.19	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		2021-06-03	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	1.32	69.9	98.9	0.066	0.072	0.999	17.28	6.21		57323

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	1.32	1.35	93.9		0.812	0.912	0.71	2.27	4.81

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	1.32	69.9	57320	2774	98.954	0.115	0.1129	0.1367	0.1529	0.1621	16.022

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]
0.379		-0.106	-0.178		-0.129

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.8
r_dihedral_angle_4_deg	23.039
r_dihedral_angle_3_deg	12.748
r_dihedral_angle_1_deg	6.785
r_lrange_it	4.713
r_lrange_other	4.666
r_scangle_it	4.151
r_scangle_other	4.15
r_rigid_bond_restr	3.867
r_scbond_it	3.782
r_scbond_other	3.78
r_mcangle_it	2.877
r_mcangle_other	2.875
r_mcbond_other	2.308
r_mcbond_it	2.304
r_angle_refined_deg	2.006
r_angle_other_deg	1.512
r_nbd_refined	0.255
r_symmetry_xyhbond_nbd_refined	0.225
r_symmetry_nbd_refined	0.202
r_symmetry_nbd_other	0.198
r_nbd_other	0.198
r_xyhbond_nbd_refined	0.18
r_nbtor_refined	0.176
r_chiral_restr	0.133
r_symmetry_nbtor_other	0.089
r_metal_ion_refined	0.069
r_bond_refined_d	0.017
r_gen_planes_refined	0.012
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2065
Nucleic Acid Atoms
Solvent Atoms	322
Heterogen Atoms	39

Software

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