3M96 | pdb_00003m96

Crystal structure of human carbonic anhydrase isozyme II with 5-{[(5-bromo-1H-benzimidazol-2-yl)sulfanyl]acetyl}-2-chlorobenzenesulfonamide

X-RAY DIFFRACTION

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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		291	Crystallization buffer was 0.1M sodium BICINE, pH 9.0, 0.2 M ammonium sulfate and 2M sodium malonate, pH 7.0 made from 1M sodium BICINE and 3.4M sodium malonate, vapor diffusion, sitting drop, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.04	39.58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.05	α = 90
b = 40.921	β = 104.14
c = 71.468	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	MARRESEARCH		2009-12-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X12	0.9443	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	1.4	28.884	99.2	0.095	0.095	22.9	9.3	46670	46297			14.3

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)
	1.4	1.48	98.1		0.253	0.253	4.4	7.4	6614

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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 3HLJ	1.4	28.47	46670	46284	4647	99.23	0.18	0.176	0.1717	0.213	0.2089	RANDOM	15.552

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]
0.12		0.11	-0.51		0.44

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.393
r_dihedral_angle_4_deg	22.122
r_dihedral_angle_3_deg	13.325
r_dihedral_angle_1_deg	6.952
r_scangle_it	4.879
r_scbond_it	3.309
r_angle_refined_deg	2.587
r_mcangle_it	2.474
r_mcbond_it	1.84
r_nbtor_refined	0.325
r_nbd_refined	0.226
r_symmetry_hbond_refined	0.212
r_symmetry_vdw_refined	0.187
r_chiral_restr	0.186
r_xyhbond_nbd_refined	0.15
r_metal_ion_refined	0.078
r_bond_refined_d	0.032
r_gen_planes_refined	0.017

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2049
Nucleic Acid Atoms
Solvent Atoms	239
Heterogen Atoms	34

Software

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