5LLG | pdb_00005llg

Crystal structure of human carbonic anhydrase isozyme II with 4-Propylthiobenzenesulfonamide

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
2.01	38.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.116	α = 90
b = 41.129	β = 104.24
c = 71.824	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-F		2014-01-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)	0.826606	PETRA III, EMBL c/o DESY	P14 (MX2)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	40.821	91.5	0.068	11.2	6.6		83155			10.684

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.12	1.18	67		0.4	1.8	5.5

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	39.74	74815	8316	91.15	0.1409	0.138	0.13	0.1671	0.16	RANDOM	17.787

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]
0.35		0.06	-0.51		0.19

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.459
r_sphericity_free	22.972
r_dihedral_angle_4_deg	20.942
r_sphericity_bonded	12.711
r_dihedral_angle_3_deg	11.9
r_rigid_bond_restr	9.243
r_dihedral_angle_1_deg	6.753
r_angle_refined_deg	2.307
r_chiral_restr	0.173
r_bond_refined_d	0.024

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.459
r_sphericity_free	22.972
r_dihedral_angle_4_deg	20.942
r_sphericity_bonded	12.711
r_dihedral_angle_3_deg	11.9
r_rigid_bond_restr	9.243
r_dihedral_angle_1_deg	6.753
r_angle_refined_deg	2.307
r_chiral_restr	0.173
r_bond_refined_d	0.024
r_gen_planes_refined	0.015

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2049
Nucleic Acid Atoms
Solvent Atoms	306
Heterogen Atoms	48

Software

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

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.