4E3D | pdb_00004e3d

Nucleophile recognition as an alternative inhibition mode for benzoic acid based carbonic anhydrase inhibitors

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3KS3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	291	3M Ammonium Sulfate, pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.09	41.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.204	α = 90
b = 41.479	β = 104.32
c = 72.119	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	BRUKER SMART 6000		2011-04-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	ENRAF-NONIUS FR571	1.54184

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	1.6	69.88	99.66			32142	32032	1	1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.6	1.642	98.84

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	3KS3	1.6	69.88	1	32032	32032	1628	99.66	0.171	0.17102	0.16887	0.17	0.21076	0.21	RANDOM	10.422

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]
		-0.01			-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.01
r_dihedral_angle_4_deg	22.302
r_dihedral_angle_3_deg	13.127
r_dihedral_angle_1_deg	6.961
r_scangle_it	4.781
r_scbond_it	3.16
r_mcangle_it	2.136
r_angle_refined_deg	2.103
r_mcbond_it	1.339
r_chiral_restr	0.157

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.01
r_dihedral_angle_4_deg	22.302
r_dihedral_angle_3_deg	13.127
r_dihedral_angle_1_deg	6.961
r_scangle_it	4.781
r_scbond_it	3.16
r_mcangle_it	2.136
r_angle_refined_deg	2.103
r_mcbond_it	1.339
r_chiral_restr	0.157
r_bond_refined_d	0.025
r_gen_planes_refined	0.013

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2049
Nucleic Acid Atoms
Solvent Atoms	178
Heterogen Atoms	39

Software

Software
Software Name	Purpose
APEX	data collection
PHASER	phasing
REFMAC	refinement
APEX	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.