4WL4

Crystal structure of human carbonic anhydrase II in complex with the 6-hydroxy-chromene-2-thione inhibitor

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3P58

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	296	1.6 M sodium citrate, Tris 50 mM

Crystal Properties
Matthews coefficient	Solvent content
2.09	41.18

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.264	α = 90
b = 41.367	β = 104.21
c = 72.276	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		2014-05-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	1.000	ESRF	ID23-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim 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	1.1	29.1	80.7	0.048	0.057	12.9	3.45		78925		-3	15.075

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.1	1.17	27.2		0.421	0.554	1.73

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3P58	1.1	29.1	75094	3814	80.74	0.11	0.109	0.1299	RANDOM	15.743

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]
0.24		-0.08	-0.15		-0.05

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	37.448
r_dihedral_angle_2_deg	34.193
r_dihedral_angle_4_deg	24.683
r_sphericity_bonded	11.081
r_dihedral_angle_3_deg	10.739
r_dihedral_angle_1_deg	6.406
r_mcangle_it	1.678
r_angle_refined_deg	1.311
r_mcbond_it	1.196
r_mcbond_other	1.195

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	37.448
r_dihedral_angle_2_deg	34.193
r_dihedral_angle_4_deg	24.683
r_sphericity_bonded	11.081
r_dihedral_angle_3_deg	10.739
r_dihedral_angle_1_deg	6.406
r_mcangle_it	1.678
r_angle_refined_deg	1.311
r_mcbond_it	1.196
r_mcbond_other	1.195
r_rigid_bond_restr	1.079
r_angle_other_deg	0.787
r_chiral_restr	0.086
r_bond_refined_d	0.007
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2027
Nucleic Acid Atoms
Solvent Atoms	395
Heterogen Atoms	36

Software

Software
Software Name	Purpose
XDS	data reduction
REFMAC	refinement
PDB_EXTRACT	data extraction
XSCALE	data scaling
MOLREP	phasing
XSCALE	data reduction

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.