6G5L | pdb_00006g5l

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

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1JD0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.2	291	Crystallization buffer: 0.1M ammonium citrate (pH 7.2), 0.2 M ammonium sulfate and 30% PEG4000

Crystal Properties
Matthews coefficient	Solvent content
2.08	40.78

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.127	α = 90
b = 74.235	β = 108.64
c = 91.527	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 PILATUS3 6M		2014-01-08	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	1.21	73.083	95.9	0.043	0.053	0.02	20.2	7	284311	284311

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)
	1.21	1.28	92.9		0.421	0.421	0.5	0.191	1.7	6.6	40120

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	1JD0	1.21	73.08	284275	28370	95.67	0.1396	0.1359	0.14	0.1734	0.17	RANDOM	20.0494

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]
-0.29		0.08	0.36		-0.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.228
r_sphericity_free	22.794
r_dihedral_angle_4_deg	17.376
r_sphericity_bonded	15.163
r_dihedral_angle_3_deg	12.059
r_rigid_bond_restr	8.235
r_dihedral_angle_1_deg	6.961
r_scbond_it	5.123
r_mcangle_it	3.699
r_mcbond_it	3.123

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.228
r_sphericity_free	22.794
r_dihedral_angle_4_deg	17.376
r_sphericity_bonded	15.163
r_dihedral_angle_3_deg	12.059
r_rigid_bond_restr	8.235
r_dihedral_angle_1_deg	6.961
r_scbond_it	5.123
r_mcangle_it	3.699
r_mcbond_it	3.123
r_angle_refined_deg	2.514
r_chiral_restr	0.185
r_bond_refined_d	0.029
r_gen_planes_refined	0.018

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8327
Nucleic Acid Atoms
Solvent Atoms	1036
Heterogen Atoms	162

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
PDB_EXTRACT	data extraction
Coot	model building
SCALA	data scaling
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.