6R6F | pdb_00006r6f

Crystal structure of human carbonic anhydrase isozyme II with 4-chloro-2-cyclohexylsulfanyl-N-(2-hydroxyethyl)-5-sulfamoyl-benzamide

X-RAY DIFFRACTION

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, 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
2.11	41.82

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.308	α = 90
b = 41.749	β = 104.19
c = 72.323	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		2015-06-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)	1.01000	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	1.2	41.017	93.2	0.118	0.133	0.053	6.7	6	71118	71118

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	1.2	1.26	90.2		0.434	0.434	0.511	0.204	1.5	6.1

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-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3HLJ	1.2	32.16	71102	4509	92.73	0.149	0.1457	0.185	RANDOM	19.0325

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]
0.06		-0.15	-0.23		0.22

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	33.191
r_dihedral_angle_2_deg	32.722
r_dihedral_angle_4_deg	21.373
r_sphericity_bonded	18.493
r_dihedral_angle_3_deg	14.152
r_dihedral_angle_1_deg	7.094
r_rigid_bond_restr	5.936
r_scbond_it	5.211
r_mcangle_it	3.522
r_mcbond_it	2.712

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	33.191
r_dihedral_angle_2_deg	32.722
r_dihedral_angle_4_deg	21.373
r_sphericity_bonded	18.493
r_dihedral_angle_3_deg	14.152
r_dihedral_angle_1_deg	7.094
r_rigid_bond_restr	5.936
r_scbond_it	5.211
r_mcangle_it	3.522
r_mcbond_it	2.712
r_angle_refined_deg	2.049
r_chiral_restr	0.141
r_bond_refined_d	0.019
r_gen_planes_refined	0.014

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2059
Nucleic Acid Atoms
Solvent Atoms	340
Heterogen Atoms	29

Software

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