8QFK | pdb_00008qfk

Human Carbonic Anhydrase II in complex with (3-((N-(4-sulfamoylbenzyl)methylsulfonamido)methyl)phenyl)glycine

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, 50 mM Tris pH 8.0

Crystal Properties
Matthews coefficient	Solvent content
2.12	42.03

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.59	α = 90
b = 41.59	β = 104.52
c = 72.48	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	0.9718	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	1.11	50	96.3	0.055	0.06	0.999	14.7	5.8		94466

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	1.11	1.14	69.4		0.462	0.557	0.756	2.3	3.2

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	1.11	50	94466	4673	96.311	0.117	0.1163	0.1162	0.1397	0.139	15.508

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]
0.036		-0.041	0.009		-0.021

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.332
r_dihedral_angle_4_deg	25.003
r_rigid_bond_restr	17.857
r_dihedral_angle_3_deg	11.712
r_dihedral_angle_1_deg	6.909
r_scangle_it	5.712
r_scangle_other	5.71
r_lrange_it	5.308
r_lrange_other	5.203
r_scbond_it	5.152
r_scbond_other	5.151
r_mcangle_other	4.108
r_mcangle_it	4.102
r_mcbond_it	2.998
r_mcbond_other	2.997
r_angle_refined_deg	2.148
r_angle_other_deg	1.593
r_symmetry_nbd_refined	0.262
r_nbd_refined	0.242
r_nbd_other	0.204
r_symmetry_nbd_other	0.199
r_xyhbond_nbd_refined	0.198
r_symmetry_xyhbond_nbd_other	0.186
r_symmetry_xyhbond_nbd_refined	0.185
r_nbtor_refined	0.18
r_chiral_restr	0.133
r_symmetry_nbtor_other	0.093
r_metal_ion_refined	0.064
r_bond_refined_d	0.018
r_gen_planes_refined	0.013
r_bond_other_d	0.005
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2038
Nucleic Acid Atoms
Solvent Atoms	316
Heterogen Atoms	35

Software

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