8QGV | pdb_00008qgv

Human Carbonic Anhydrase I in complex with 4-(5-acetyl-6-methyl-2-oxo-1,2,3,4-tetrahydropyrimidin-4-yl)benzenesulfonamide

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 8.5-9.0

Crystal Properties
Matthews coefficient	Solvent content
2.34	47.47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.94	α = 90
b = 71.14	β = 90
c = 120.92	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		2023-06-26	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	1.84	50	100	0.122	0.127	0.999	22.21	12.76		48159

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	1.84	1.88	100		1.762	1.835	0.781	2.28	12.8

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	1.84	50	48159	2376	99.94	0.2	0.1978	0.2063	0.2403	0.2501	31.709

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]
0.214			1.361		-1.575

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.45
r_dihedral_angle_4_deg	16.866
r_dihedral_angle_3_deg	14.832
r_dihedral_angle_1_deg	7.535
r_lrange_it	6.224
r_lrange_other	6.224
r_scangle_it	4.952
r_scangle_other	4.951
r_mcangle_it	3.631
r_mcangle_other	3.63
r_scbond_it	3.407
r_scbond_other	3.407
r_mcbond_other	2.75
r_mcbond_it	2.749
r_angle_refined_deg	1.658
r_angle_other_deg	1.34
r_nbd_other	0.216
r_nbd_refined	0.202
r_symmetry_nbd_other	0.187
r_nbtor_refined	0.166
r_symmetry_xyhbond_nbd_refined	0.15
r_symmetry_nbd_refined	0.137
r_xyhbond_nbd_refined	0.136
r_symmetry_nbtor_other	0.082
r_metal_ion_refined	0.079
r_chiral_restr	0.078
r_xyhbond_nbd_other	0.045
r_bond_refined_d	0.01
r_gen_planes_refined	0.01
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	215
Heterogen Atoms	48

Software

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