9H81 | pdb_00009h81

human carbonic anhydrase I 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	1JV0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	28% PEG4000, 0.2 M sodium acetate, 0.1 M Tris pH 9.0

Crystal Properties
Matthews coefficient	Solvent content
2.35	47.68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.625	α = 90
b = 71.232	β = 90
c = 121.87	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 PILATUS 6M		2022-07-23	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	2.35	61.5	100	0.12	0.132	0.998	13.5	10.5		23430

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	2.35	2.43	100		0.655	0.715	0.943	3.3	10.6

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	2.35	61.5	23296	1108	99.602	0.199	0.1955	0.2018	0.2624	0.2613	34.359

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]
0.006			0.171		-0.177

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.665
r_dihedral_angle_4_deg	20.377
r_dihedral_angle_3_deg	15.282
r_dihedral_angle_1_deg	7.963
r_lrange_it	7.899
r_lrange_other	7.896
r_scangle_it	4.993
r_scangle_other	4.993
r_mcangle_other	3.808
r_mcangle_it	3.807
r_scbond_it	3.122
r_scbond_other	3.121
r_mcbond_it	2.555
r_mcbond_other	2.555
r_angle_refined_deg	1.52
r_angle_other_deg	1.254
r_nbd_other	0.222
r_symmetry_xyhbond_nbd_refined	0.207
r_nbd_refined	0.189
r_symmetry_nbd_other	0.185
r_symmetry_nbd_refined	0.166
r_nbtor_refined	0.164
r_xyhbond_nbd_refined	0.141
r_metal_ion_refined	0.108
r_symmetry_nbtor_other	0.079
r_chiral_restr	0.071
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4016
Nucleic Acid Atoms
Solvent Atoms	83
Heterogen Atoms	58

Software

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