3M2N | pdb_00003m2n

Crystal structure of human carbonic anhydrase isozyme II with 4-{2-[N-(6-chloro-5-nitropyrimidin-4-yl)amino]ethyl}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		293	0.1M Na-Bicine pH 9, 2M Na-Malonate pH7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.06	40.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.041	α = 90
b = 41.253	β = 104.74
c = 71.858	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	2009-12-20	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	1.65	41.24	100	0.076	0.076	26.3	9.6	28936	28936			13.8

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	1.65	1.74	100		0.211	0.211	8.6	6.6	4178

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	1.65	39.78	25992	25992	2928	100	0.15951	0.15951	0.15453	0.1526	0.20304	0.2017	RANDOM	14.049

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]
0.64		0.13	-0.69		0.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.274
r_dihedral_angle_4_deg	22.789
r_dihedral_angle_3_deg	14.348
r_dihedral_angle_1_deg	7.273
r_scangle_it	4.79
r_scbond_it	3.478
r_angle_refined_deg	2.443
r_mcangle_it	2.156
r_mcbond_it	1.521
r_nbtor_refined	0.316

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.274
r_dihedral_angle_4_deg	22.789
r_dihedral_angle_3_deg	14.348
r_dihedral_angle_1_deg	7.273
r_scangle_it	4.79
r_scbond_it	3.478
r_angle_refined_deg	2.443
r_mcangle_it	2.156
r_mcbond_it	1.521
r_nbtor_refined	0.316
r_symmetry_vdw_refined	0.266
r_nbd_refined	0.237
r_xyhbond_nbd_refined	0.182
r_symmetry_hbond_refined	0.172
r_chiral_restr	0.163
r_metal_ion_refined	0.099
r_bond_refined_d	0.029
r_gen_planes_refined	0.014

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2059
Nucleic Acid Atoms
Solvent Atoms	370
Heterogen Atoms	43

Software

Software
Software Name	Purpose
MAR345	data collection
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

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.