7M24 | pdb_00007m24

Human carbonic anhydrase II in complex with (R)-rosiglitazone

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6ODZ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.3	293	Protein concentration was 4 mg/mL; equal volumes (250 nL) of protein plus reservoir were added to the plate; the reservoir was 1.5 M tri-potassium citrate, 0.1 M tris buffer at pH 8.3.

Crystal Properties
Matthews coefficient	Solvent content
2.09	41.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.574	α = 90
b = 41.282	β = 104.416
c = 71.932	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 EIGER X 9M		2019-09-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX1	0.953656	Australian Synchrotron	MX1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim 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	1.3	41.28	99.7	0.064	0.04	0.999	14.6	6.6		59530

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.3	1.32			0.443	0.294	0.865

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	6ODZ	1.3	40.165	59512	2935	99.627	0.117	0.1158	0.12	0.1457	0.15	12.774

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]
-0.253		0.173	-0.439		0.533

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.99
r_dihedral_angle_4_deg	21.366
r_dihedral_angle_3_deg	11.457
r_dihedral_angle_1_deg	7.161
r_lrange_it	2.777
r_lrange_other	2.288
r_scangle_it	2.027
r_scangle_other	2.027
r_angle_refined_deg	1.623
r_scbond_it	1.556
r_scbond_other	1.556
r_mcangle_other	1.527
r_mcangle_it	1.525
r_angle_other_deg	1.468
r_rigid_bond_restr	1.156
r_mcbond_other	1.136
r_mcbond_it	1.135
r_symmetry_nbd_refined	0.255
r_nbd_refined	0.233
r_xyhbond_nbd_refined	0.208
r_symmetry_nbd_other	0.197
r_nbd_other	0.197
r_nbtor_refined	0.173
r_symmetry_xyhbond_nbd_refined	0.161
r_symmetry_xyhbond_nbd_other	0.125
r_chiral_restr	0.09
r_symmetry_nbtor_other	0.081
r_metal_ion_refined	0.064
r_bond_refined_d	0.01
r_gen_planes_refined	0.009
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2059
Nucleic Acid Atoms
Solvent Atoms	313
Heterogen Atoms	26

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing