6G6T | pdb_00006g6t

Crystal structure of human carbonic anhydrase isozyme II with N-butyl-2,4-dichloro-5-sulfamoyl-benzamide

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4HT0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	291	Crystallization buffer: 0.1M sodium bicine (pH 9), 0.2M ammonium sulfate and 2M sodium malonate (pH 7)

Crystal Properties
Matthews coefficient	Solvent content
2.07	40.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.057	α = 90
b = 41.196	β = 104.19
c = 72.094	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	PIXEL	DECTRIS PILATUS 6M		2013-05-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)	0.975522	PETRA III, EMBL c/o DESY	P14 (MX2)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	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	1.12	41.196	94.3	0.052	0.066	0.025	28.4	6.4		86201

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.123	1.18	73.4		0.064	0.064	0.089	0.038	11	5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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	4HT0	1.12	39.71	86179	8706	94.3	0.1467	0.1433	0.14	0.1774	0.18	RANDOM	16.1384

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]
0.5		0.07	-0.53

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35
r_sphericity_free	22.362
r_dihedral_angle_4_deg	19.48
r_sphericity_bonded	14.823
r_dihedral_angle_3_deg	13.91
r_rigid_bond_restr	10.839
r_dihedral_angle_1_deg	6.107
r_scbond_it	3.742
r_angle_refined_deg	2.837
r_mcangle_it	2.502

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35
r_sphericity_free	22.362
r_dihedral_angle_4_deg	19.48
r_sphericity_bonded	14.823
r_dihedral_angle_3_deg	13.91
r_rigid_bond_restr	10.839
r_dihedral_angle_1_deg	6.107
r_scbond_it	3.742
r_angle_refined_deg	2.837
r_mcangle_it	2.502
r_mcbond_it	2.343
r_chiral_restr	0.185
r_bond_refined_d	0.03
r_gen_planes_refined	0.018

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2034
Nucleic Acid Atoms
Solvent Atoms	328
Heterogen Atoms	35

Software

Software
Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
MOLREP	phasing
Coot	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.