9FPS | pdb_00009fps

Crystal structure of carbonic anhydrase II with methyl 4-methylsulfanyl-3-sulfamoyl-benzoate

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4HT0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291	0.1M sodium bicine (pH 9) and 2M sodium malonate (pH 7)

Crystal Properties
Matthews coefficient	Solvent content
2.03	38.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.314	α = 90
b = 41.169	β = 104.4
c = 72.026	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		2021-12-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)	0.976200	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	1.39	40.985	97.6	0.036	0.044	0.017	24.2	7	47284	47284

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	1.39	1.47	94.9		0.377	0.377	0.443	0.168	1.9	6.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	1.39	39.94	42563	4706	97.23	0.1464	0.1416	0.1443	0.1896	0.1799	RANDOM	21.784

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]
1.22		0.98	-0.45		-1.12

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.712
r_sphericity_free	29.4
r_dihedral_angle_4_deg	23.657
r_sphericity_bonded	17.192
r_dihedral_angle_3_deg	11.638
r_dihedral_angle_1_deg	7.016
r_rigid_bond_restr	4.969
r_angle_refined_deg	2.023
r_chiral_restr	0.133
r_bond_refined_d	0.014

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.712
r_sphericity_free	29.4
r_dihedral_angle_4_deg	23.657
r_sphericity_bonded	17.192
r_dihedral_angle_3_deg	11.638
r_dihedral_angle_1_deg	7.016
r_rigid_bond_restr	4.969
r_angle_refined_deg	2.023
r_chiral_restr	0.133
r_bond_refined_d	0.014
r_gen_planes_refined	0.014

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2041
Nucleic Acid Atoms
Solvent Atoms	344
Heterogen Atoms	37

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
Coot	model building
MOLREP	phasing
XDS	data reduction

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.