4WW6 | pdb_00004ww6

Crystal structure of human carbonic anhydrase isozyme II with 2,3,5,6-Tetrafluoro-4-(propylthio)benzenesulfonamide

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3HLJ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	291	Crystallization buffer was 0.1M sodium BICINE, pH 9, 0.25 M ammonium sulfate and 2M sodium malonate pH 7 made from 1M sodium BICINE and 3.4M sodium malonate

Crystal Properties
Matthews coefficient	Solvent content
2	38.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.214	α = 90
b = 41.026	β = 104.29
c = 71.774	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		2013-05-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)	0.826606	PETRA III, EMBL c/o DESY	P13 (MX1)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	1.06	69.554	95.4	0.041	0.05	0.019	17.9	6.6	102717	102717			8.784

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.06	1.12	83		0.35	0.35	0.43	0.17	2.2	5.8	12952

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	MOLECULAR REPLACEMENT	THROUGHOUT	3HLJ	1.06	40.91	102697	10363	95.17	0.131	0.128	0.13	0.151	0.15	RANDOM	15.737

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]
0.02		-0.1	-0.27		0.21

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.618
r_sphericity_free	20.884
r_dihedral_angle_4_deg	20.597
r_dihedral_angle_3_deg	11.976
r_sphericity_bonded	9.795
r_rigid_bond_restr	8.835
r_dihedral_angle_1_deg	7.167
r_angle_refined_deg	2.417
r_chiral_restr	0.162
r_bond_refined_d	0.024

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.618
r_sphericity_free	20.884
r_dihedral_angle_4_deg	20.597
r_dihedral_angle_3_deg	11.976
r_sphericity_bonded	9.795
r_rigid_bond_restr	8.835
r_dihedral_angle_1_deg	7.167
r_angle_refined_deg	2.417
r_chiral_restr	0.162
r_bond_refined_d	0.024
r_gen_planes_refined	0.015

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2049
Nucleic Acid Atoms
Solvent Atoms	268
Heterogen Atoms	67

Software

Software
Software Name	Purpose
XDS	data reduction
PDB_EXTRACT	data extraction
SCALA	data scaling
Coot	model building
MOLREP	phasing
REFMAC	refinement

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.