6G9U | pdb_00006g9u

Three dimensional structure of human carbonic anhydrase IX in complex with sulfonamide

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5FL4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.5	294	1.0 M DI-AMMONIUM HYDROGEN PHOSPHATE, 0.1 M SODIUM ACETATE PH 4.5, PROTEIN 10 MG/ML, 5-10 MM INHIBITOR (STOCK SOLUTION WAS 100 MM INHIBITOR DISSOLVED IN 100% DIMETHYL SULFOXIDE)

Crystal Properties
Matthews coefficient	Solvent content
3.43	64.14

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 152.38	α = 90
b = 152.38	β = 90
c = 171.84	γ = 120

Symmetry
Space Group	H 3

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		2018-01-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.91840	BESSY	14.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.75	76.19	97.6	0.055	9.3	3		146413			23.1

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	1.75	1.84	95.5		0.502	2	2.9

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	5FL4	1.75	76.19	139211	7170	97.58	0.16871	0.16768	0.18	0.18895	0.19	RANDOM	32.277

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]
0.43	0.22		0.43		-1.4

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.989
r_dihedral_angle_4_deg	15.385
r_dihedral_angle_3_deg	11.795
r_long_range_B_refined	6.083
r_long_range_B_other	5.887
r_dihedral_angle_1_deg	5.708
r_scangle_other	3.961
r_mcangle_it	2.938
r_mcangle_other	2.938
r_scbond_it	2.45
r_scbond_other	2.45
r_mcbond_it	1.879
r_mcbond_other	1.877
r_angle_refined_deg	1.401
r_angle_other_deg	0.916
r_chiral_restr	0.076
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_gen_planes_other	0.004
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7388
Nucleic Acid Atoms
Solvent Atoms	880
Heterogen Atoms	140

Software

Software
Software Name	Purpose
REFMAC	refinement
SCALA	data scaling