9FPR | pdb_00009fpr

Crystal structure of carbonic anhydrase II with methyl 4-(2-phenylethylsulfanyl)-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, 0.2 M ammonium sulfate and 2M sodium malonate pH 7 made from 1M sodium BICINE and 3.4M sodium malonate

Crystal Properties
Matthews coefficient	Solvent content
2.03	39.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.332	α = 90
b = 41.317	β = 104.51
c = 72.05	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	1.46	40.981	98.7	0.047	0.056	0.021	19.6	7	41447	41447

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	1.46	1.54	97.7		0.389	0.389	0.449	0.167	1.7	6.9

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	1.46	39.98	37425	4008	98.37	0.147	0.1406	0.1501	0.2091	0.1979	RANDOM	20.098

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]
0.08		0.2	0.21		-0.35

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.774
r_sphericity_free	27.204
r_dihedral_angle_4_deg	22.209
r_sphericity_bonded	15.313
r_dihedral_angle_3_deg	12.858
r_dihedral_angle_1_deg	7.047
r_rigid_bond_restr	4.776
r_angle_refined_deg	2.037
r_chiral_restr	0.155
r_gen_planes_refined	0.015

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.774
r_sphericity_free	27.204
r_dihedral_angle_4_deg	22.209
r_sphericity_bonded	15.313
r_dihedral_angle_3_deg	12.858
r_dihedral_angle_1_deg	7.047
r_rigid_bond_restr	4.776
r_angle_refined_deg	2.037
r_chiral_restr	0.155
r_gen_planes_refined	0.015
r_bond_refined_d	0.014

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2039
Nucleic Acid Atoms
Solvent Atoms	348
Heterogen Atoms	28

Software

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

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.