6R6Y | pdb_00006r6y

Crystal structure of human carbonic anhydrase isozyme XII 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	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 26% PEG4000

Crystal Properties
Matthews coefficient	Solvent content
2.08	40.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.335	α = 90
b = 74.192	β = 108.65
c = 91.634	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		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)	0.97552	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	1.38	74.192	98.8	0.049	0.059	0.022	18.1	6.9	198797	198797

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	1.38	1.45	98.8		0.343	0.343	0.406	0.156	2.1	6.7

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	1JD0	1.38	73.28	198753	19765	98.73	0.1641	0.1616	0.1873	RANDOM	17.0663

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]
-0.27		0.16	-0.06		0.19

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.48
r_dihedral_angle_4_deg	14.093
r_dihedral_angle_3_deg	12.525
r_dihedral_angle_1_deg	7.079
r_scbond_it	2.858
r_mcangle_it	2.298
r_angle_refined_deg	1.943
r_mcbond_it	1.556
r_chiral_restr	0.119
r_bond_refined_d	0.013

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.48
r_dihedral_angle_4_deg	14.093
r_dihedral_angle_3_deg	12.525
r_dihedral_angle_1_deg	7.079
r_scbond_it	2.858
r_mcangle_it	2.298
r_angle_refined_deg	1.943
r_mcbond_it	1.556
r_chiral_restr	0.119
r_bond_refined_d	0.013
r_gen_planes_refined	0.013

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8390
Nucleic Acid Atoms
Solvent Atoms	1150
Heterogen Atoms	140

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	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.