4Q6D | pdb_00004q6d

Crystal structure of human carbonic anhydrase isozyme II with 4-[(Z)-azepan-1-yldiazenyl]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	7	291	Crystallization buffer was 0.1M sodium BICINE, pH 9, 0.2 M ammonium sulfate and 2M sodium malonate pH 7 made from 1M sodium BICINE and 3.4M sodium malonate, VAPOR DIFFUSION, SITTING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.01	38.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.125	α = 90
b = 41.195	β = 104.19
c = 71.813	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	PSI PILATUS 6M		2014-01-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)	0.826606	PETRA III, EMBL c/o DESY	P13 (MX1)

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	1.12	41.195	95.8	0.076	0.076	13.6	6.5		87368			9.25

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	1.12	1.18	80.2		0.166	0.166	3.8	5.1	10618

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	1.12	39.73	87346	87346	8792	95.77	0.131	0.131	0.128	0.13	0.154	0.15	RANDOM	16.965

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]
0.09		-0.01	-0.19		0.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.502
r_sphericity_free	23.139
r_dihedral_angle_4_deg	19.99
r_dihedral_angle_3_deg	12.641
r_sphericity_bonded	11.196
r_rigid_bond_restr	10.008
r_dihedral_angle_1_deg	6.761
r_angle_refined_deg	2.605
r_chiral_restr	0.154
r_bond_refined_d	0.025

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.502
r_sphericity_free	23.139
r_dihedral_angle_4_deg	19.99
r_dihedral_angle_3_deg	12.641
r_sphericity_bonded	11.196
r_rigid_bond_restr	10.008
r_dihedral_angle_1_deg	6.761
r_angle_refined_deg	2.605
r_chiral_restr	0.154
r_bond_refined_d	0.025
r_gen_planes_refined	0.016

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2049
Nucleic Acid Atoms
Solvent Atoms	299
Heterogen Atoms	35

Software

Software
Software Name	Purpose
REFMAC	refinement
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.