6G3Q | pdb_00006g3q

Crystal structure of human carbonic anhydrase II in complex with the inhibitor famotidine

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	8	296	1.5 M sodium citrate, Tris 50 mM

Crystal Properties
Matthews coefficient	Solvent content
2.09	41.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.316	α = 90
b = 41.439	β = 104.34
c = 72.112	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 PILATUS3 2M		2018-03-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID30B	0.827	ESRF	ID30B

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim 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	1.01	41	88.6	0.038	0.048	0.998	10.8	2.516		112412			14.189

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.01	1.08	65.1		0.601	0.765	0.639	1.35	2.374

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	FOURIER SYNTHESIS	THROUGHOUT	4FIK	1.01	41	106958	5448	88.67	0.1283	0.1271	0.1266	0.1515	0.1508	RANDOM	17.115

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		0.14	-0.19		0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	42.72
r_dihedral_angle_2_deg	35.756
r_dihedral_angle_4_deg	23.951
r_dihedral_angle_3_deg	12.511
r_sphericity_bonded	10.512
r_dihedral_angle_1_deg	6.405
r_rigid_bond_restr	2.638
r_angle_refined_deg	1.427
r_angle_other_deg	0.841
r_chiral_restr	0.082

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	42.72
r_dihedral_angle_2_deg	35.756
r_dihedral_angle_4_deg	23.951
r_dihedral_angle_3_deg	12.511
r_sphericity_bonded	10.512
r_dihedral_angle_1_deg	6.405
r_rigid_bond_restr	2.638
r_angle_refined_deg	1.427
r_angle_other_deg	0.841
r_chiral_restr	0.082
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2059
Nucleic Acid Atoms
Solvent Atoms	432
Heterogen Atoms	43

Software

Software
Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
REFMAC	phasing

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.