3S8X | pdb_00003s8x

Crystal structure of human carbonic anhydrase isozyme II with 4-{[(4-methyl-6-oxo-1,6-dihydro-2-pyrimidinyl)sulfanyl]acetyl}benzenesulfonamide

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	9	298	Na-Bicine 0.1M pH 9, Na-Malonate 2.2M pH 7, VAPOR DIFFUSION, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.07	40.13

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.208	α = 90
b = 41.18	β = 104.29
c = 71.918	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	Detector swing-out angle up to 30 degrees	2010-11-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X12	0.9748	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	1.3	41.18	95.9	0.064	0.064	26.2	7.6		56499			12.15

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	1.3	1.37	93.6		0.38	0.38	2	7.7	8022

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 (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	3HLJ	1.3	39.84	56499	56478	5694	95.53	0.146	0.142	0.1375	0.179	0.176	RANDOM	16.21

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]
-0.56			0.54		0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.159
r_dihedral_angle_4_deg	22.139
r_sphericity_free	15.581
r_dihedral_angle_3_deg	12.968
r_sphericity_bonded	9.391
r_dihedral_angle_1_deg	6.606
r_scangle_it	6.284
r_scbond_it	4.992
r_mcangle_it	3.836
r_rigid_bond_restr	3.305
r_mcbond_it	2.928
r_angle_refined_deg	2.348
r_nbtor_refined	0.322
r_nbd_refined	0.226
r_chiral_restr	0.191
r_symmetry_vdw_refined	0.19
r_symmetry_hbond_refined	0.189
r_xyhbond_nbd_refined	0.149
r_metal_ion_refined	0.083
r_bond_refined_d	0.028
r_gen_planes_refined	0.015

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2049
Nucleic Acid Atoms
Solvent Atoms	248
Heterogen Atoms	42

Software

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