3M67 | pdb_00003m67

Crystal structure of human carbonic anhydrase isozyme II with 2-chloro-5-[(6,7-dihydro-1H-[1,4]dioxino[2,3-f]benzimidazol-2-ylsulfanyl)acetyl]benzenesulfonamide

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2NNO	PDB ENTRY 2NNO

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	293	0.1M Na-bicine pH 9.0, 2M Na-Malonate pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.04	39.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.972	α = 90
b = 41.007	β = 104.43
c = 71.681	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	CCD	MAR CCD 165 mm	Bent, vertically focussing mirror	2009-12-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X13	0.8120	EMBL/DESY, HAMBURG	X13

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	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	1.8	40.656	99.3	0.052	0.052	31.5	7.5	22174	22019			19.3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.8	1.9	99		0.222	0.222	7	7.6	3191

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	PDB ENTRY 2NNO	1.8	25.13	22008	2209	99.32	0.181	0.176	0.17	0.228	0.23	RANDOM	18.913

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]
-0.04		0.11	-1		1.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.827
r_dihedral_angle_4_deg	17.316
r_dihedral_angle_3_deg	14.909
r_dihedral_angle_1_deg	6.984
r_scangle_it	4.208
r_scbond_it	3.017
r_angle_refined_deg	2.061
r_mcangle_it	2.032
r_mcbond_it	1.439
r_nbtor_refined	0.309

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.827
r_dihedral_angle_4_deg	17.316
r_dihedral_angle_3_deg	14.909
r_dihedral_angle_1_deg	6.984
r_scangle_it	4.208
r_scbond_it	3.017
r_angle_refined_deg	2.061
r_mcangle_it	2.032
r_mcbond_it	1.439
r_nbtor_refined	0.309
r_symmetry_hbond_refined	0.244
r_symmetry_vdw_refined	0.242
r_nbd_refined	0.222
r_xyhbond_nbd_refined	0.164
r_chiral_restr	0.158
r_metal_ion_refined	0.062
r_bond_refined_d	0.027
r_gen_planes_refined	0.012

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2049
Nucleic Acid Atoms
Solvent Atoms	158
Heterogen Atoms	37

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PDB_EXTRACT	data extraction

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.