3MHL

Crystal structure of human carbonic anhydrase isozyme II with 4-{[N-(6-methoxy-5-nitropyrimidin-4-yl)amino]methyl}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	9	293	0.1M Na-bicine pH 9, 2.6M Na-malonate pH 7, VAPOR DIFFUSION, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
1.99	38.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.712	α = 90
b = 40.677	β = 104.13
c = 70.716	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	MARMOSAIC 225 mm CCD	Vertically focussing mirror	2009-12-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X12	0.9720	EMBL/DESY, HAMBURG	X12

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	1.9	40.689	100	0.076	0.076	37.9	15.3	18388	18388			24.1

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)
	1.9	2	100		0.252	0.252	7.5	11.5	2642

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2NNO	1.9	40.46	18377	18377	1849	100	0.168	0.168	0.162	0.219	RANDOM	25.533

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]
-0.31		-0.71	-1.43		1.39

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.629
r_dihedral_angle_3_deg	15.689
r_dihedral_angle_4_deg	15.074
r_dihedral_angle_1_deg	7.2
r_scangle_it	4.994
r_scbond_it	3.528
r_mcangle_it	2.219
r_angle_refined_deg	1.998
r_mcbond_it	1.483
r_chiral_restr	0.345

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.629
r_dihedral_angle_3_deg	15.689
r_dihedral_angle_4_deg	15.074
r_dihedral_angle_1_deg	7.2
r_scangle_it	4.994
r_scbond_it	3.528
r_mcangle_it	2.219
r_angle_refined_deg	1.998
r_mcbond_it	1.483
r_chiral_restr	0.345
r_nbtor_refined	0.321
r_symmetry_hbond_refined	0.231
r_nbd_refined	0.207
r_symmetry_vdw_refined	0.192
r_xyhbond_nbd_refined	0.15
r_metal_ion_refined	0.07
r_bond_refined_d	0.023
r_gen_planes_refined	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2049
Nucleic Acid Atoms
Solvent Atoms	117
Heterogen Atoms	32

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
O	model building

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.