9GU7 | pdb_00009gu7

Human carbonic anhydrase II complexed with N-phenyl-2-(1H-tetrazol-5-yl)acetamide

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	295	1.5 M sodium citrate, 0.1 M Tris pH 8.0

Crystal Properties
Matthews coefficient	Solvent content
2.13	42.13

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.455	α = 90
b = 41.681	β = 104.603
c = 72.709	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		2024-06-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ELETTRA BEAMLINE 11.2C	1.00	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	1.35	35.89	88.8	0.043	0.047	0.999	22.6	5.8		48117

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	1.35	1.37	50.1		0.43	0.51	0.788	2.8	3.3

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	1.35	35.89	47936	2414	88.34	0.124	0.1223	0.1345	0.165	0.1701	16.28

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]
-0.815		0.055	0.238		0.483

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.815
r_dihedral_angle_4_deg	23.116
r_dihedral_angle_3_deg	12.463
r_dihedral_angle_1_deg	7.046
r_scangle_it	6.538
r_scangle_other	6.536
r_scbond_it	6.019
r_scbond_other	6.016
r_lrange_it	4.793
r_lrange_other	4.693
r_rigid_bond_restr	4.553
r_mcangle_other	3.11
r_mcangle_it	3.01
r_mcbond_it	2.717
r_mcbond_other	2.416
r_angle_refined_deg	1.952
r_angle_other_deg	1.524
r_symmetry_nbd_refined	0.34
r_nbd_refined	0.239
r_nbd_other	0.202
r_symmetry_nbd_other	0.2
r_nbtor_refined	0.177
r_symmetry_xyhbond_nbd_refined	0.165
r_xyhbond_nbd_refined	0.142
r_chiral_restr	0.116
r_metal_ion_refined	0.091
r_symmetry_nbtor_other	0.087
r_bond_refined_d	0.017
r_gen_planes_refined	0.013
r_gen_planes_other	0.003
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2056
Nucleic Acid Atoms
Solvent Atoms	286
Heterogen Atoms	20

Software

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