6YKC | pdb_00006ykc

Metala-Carborane di-ethyl-sulfonamide (trans isomer) in complex with CA IX mimic

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5OGP

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.8	291	1.6 M sodium citrate, 50 mM Tris-H2SO4

Crystal Properties
Matthews coefficient	Solvent content
2.07	40.68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.958	α = 90
b = 41.21	β = 103.86
c = 72.138	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		2017-04-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.9184	BESSY	14.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	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	39.57	95.1	0.064	0.077	0.999	9.83	3.249		71539			17.797

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.2	1.27	78.4		1.095	1.364	0.413	0.84	2.635

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	FOURIER SYNTHESIS	THROUGHOUT	5OGP	1.2	39.57	69438	2100	95.09	0.1484	0.1474	0.15	0.179	0.1809	RANDOM	18.981

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]
-0.82		-0.11	0.48		0.34

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.765
r_sphericity_free	24.122
r_dihedral_angle_4_deg	18.446
r_rigid_bond_restr	15.812
r_sphericity_bonded	12.184
r_dihedral_angle_3_deg	11.718
r_dihedral_angle_1_deg	6.781
r_angle_other_deg	2.496
r_angle_refined_deg	1.722
r_chiral_restr	0.11
r_bond_refined_d	0.016
r_gen_planes_refined	0.011
r_bond_other_d	0.009
r_gen_planes_other	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2029
Nucleic Acid Atoms
Solvent Atoms	304
Heterogen Atoms	71

Software

Software
Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
FFT	phasing