3SBH | pdb_00003sbh

Crystal structure of human carbonic anhydrase isozyme II with 4-{[(4,6-dimethyl-2-pyrimidinyl)sulfanyl]acetyl}benzenesulfonamide

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	9	298	0.1M Na-bicine pH 9, 2M Na-malonate pH 7.55, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.1	40.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.093	α = 90
b = 41.09	β = 104.17
c = 71.839	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	IMAGE PLATE	MAR555 FLAT PANEL	Bent, vertically focussing	2010-11-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X11	0.8174	EMBL/DESY, HAMBURG	X11

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	28.55	97.7	0.058	0.058	30.7	7.6		28165			16.2

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	96.8		0.278	0.278	2.1	7.7	4038

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	MR	THROUGHOUT	PDB entry 3HLJ	1.65	25.23	28153	28153	2850	97.37	0.178	0.178	0.172	0.17	0.228	0.22	RANDOM	15.461

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]
0.11		-0.06	-0.37		0.23

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.403
r_dihedral_angle_4_deg	23.322
r_dihedral_angle_3_deg	13.67
r_dihedral_angle_1_deg	7.146
r_scangle_it	4.597
r_scbond_it	3.283
r_angle_refined_deg	2.335
r_mcangle_it	2.257
r_mcbond_it	1.538
r_nbtor_refined	0.316

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.403
r_dihedral_angle_4_deg	23.322
r_dihedral_angle_3_deg	13.67
r_dihedral_angle_1_deg	7.146
r_scangle_it	4.597
r_scbond_it	3.283
r_angle_refined_deg	2.335
r_mcangle_it	2.257
r_mcbond_it	1.538
r_nbtor_refined	0.316
r_symmetry_vdw_refined	0.233
r_nbd_refined	0.227
r_symmetry_hbond_refined	0.217
r_chiral_restr	0.174
r_xyhbond_nbd_refined	0.145
r_metal_ion_refined	0.039
r_bond_refined_d	0.029
r_gen_planes_refined	0.013

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2065
Nucleic Acid Atoms
Solvent Atoms	303
Heterogen Atoms	50

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.