3PYK | pdb_00003pyk

Human Carbonic Anhydrase II as Host for Pianostool Complexes Bearing a Sulfonamide Anchor

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2CBA	PDB entry 2cba

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	277	3 uL protein solution (20 mg/mL lyophilized hCAII in 50 mM Tris-sulfate, 1 mM methyl mercuric acetate) and 5 uL precipitating buffer (2.6 M ammonium sulfate, 50 mM Tris-sulfate were mixed and equilibrated against 500 uL precipitating buffer. Single crystals were transferred into a cross-linking buffer, which was prepared from 10 uL precipitating buffer and 5 uL glutaraldehyde solution (0.8 % glutaraldehyde, 4 M ammonium sulfate, 50 mM Tris-sulfate) and equilibrated for 18 h. Cross-linked crystals were transferred into soaking buffer (9 uL precipitating buffer, 0.5 uL 60 mM {(6-benzene)Ru(bispy 3)Cl}+ in DMSO) and equilibrated for 54 h, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.09	41.24

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.099	α = 90
b = 41.493	β = 104.33
c = 72.382	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	CCD	MARMOSAIC 225 mm CCD		2011-04-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SEALED TUBE	OTHER	1.0

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.3	30.6	96.9				59007	2	2

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	1.3	1.334	91.2		0.309	2.8	2.7

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-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 2cba	1.3	30.6	59007	2984	98.74	0.12947	0.12756	0.14	0.16471	0.17	RANDOM	12.373

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]
-0.04		-0.28	0.15		-0.26

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.962
r_dihedral_angle_4_deg	17.319
r_dihedral_angle_3_deg	12.195
r_scangle_it	8.349
r_dihedral_angle_1_deg	6.622
r_scbond_it	6.395
r_mcangle_it	4.386
r_mcbond_it	3.195
r_rigid_bond_restr	2.895
r_angle_refined_deg	1.454
r_mcbond_other	1.233
r_angle_other_deg	0.87
r_chiral_restr	0.088
r_bond_refined_d	0.01
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2058
Nucleic Acid Atoms
Solvent Atoms	420
Heterogen Atoms	48

Software

Software
Software Name	Purpose
MAR345dtb	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling