6XXT | pdb_00006xxt

The crystal structure of hCA II in complex with a 4-(4-aroylpiperazine-1-carbonyl)benzenesulfonamide derivative.

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1CA2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	293	1.2 M sodium citrate 0.1 M Tris-HCl

Crystal Properties
Matthews coefficient	Solvent content
2.08	40.89

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.333	α = 90
b = 41.455	β = 104.26
c = 72.131	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 PILATUS3 S 6M		2019-10-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ELETTRA BEAMLINE 5.2R	1.0	ELETTRA	5.2R

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	1.05	50	99.2	0.072	0.078	0.031	12.8	5.8		112517

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.05	1.07	86.9		0.277	0.323	0.159	0.901		3.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	1CA2	1.05	35.68	111103	1144	99.22	0.1349	0.1348	0.14	0.1455	0.15	RANDOM	10.499

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]
0.78		-0.44	1.06		-1.43

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.082
r_dihedral_angle_4_deg	22.078
r_dihedral_angle_3_deg	11.124
r_dihedral_angle_1_deg	6.942
r_rigid_bond_restr	3.043
r_angle_refined_deg	1.522
r_angle_other_deg	1.456
r_chiral_restr	0.087
r_bond_refined_d	0.008
r_gen_planes_refined	0.008

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.082
r_dihedral_angle_4_deg	22.078
r_dihedral_angle_3_deg	11.124
r_dihedral_angle_1_deg	6.942
r_rigid_bond_restr	3.043
r_angle_refined_deg	1.522
r_angle_other_deg	1.456
r_chiral_restr	0.087
r_bond_refined_d	0.008
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2067
Nucleic Acid Atoms
Solvent Atoms	271
Heterogen Atoms	59

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
REFMAC	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.