6G3Q

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4FIK 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION82961.5 M sodium citrate, Tris 50 mM
Crystal Properties
Matthews coefficientSolvent content
2.0941.19

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.316α = 90
b = 41.439β = 104.34
c = 72.112γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 2M2018-03-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID30B0.827ESRFID30B

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.014188.60.0380.0480.99810.82.51611241214.189
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)RedundancyNumber Unique Reflections (All)
11.011.0865.10.6010.7650.6391.352.374

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT4FIK1.0141106958544888.670.12830.12710.1515RANDOM17.115
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]
0.080.14-0.190.03
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free42.72
r_dihedral_angle_2_deg35.756
r_dihedral_angle_4_deg23.951
r_dihedral_angle_3_deg12.511
r_sphericity_bonded10.512
r_dihedral_angle_1_deg6.405
r_rigid_bond_restr2.638
r_angle_refined_deg1.427
r_angle_other_deg0.841
r_chiral_restr0.082
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free42.72
r_dihedral_angle_2_deg35.756
r_dihedral_angle_4_deg23.951
r_dihedral_angle_3_deg12.511
r_sphericity_bonded10.512
r_dihedral_angle_1_deg6.405
r_rigid_bond_restr2.638
r_angle_refined_deg1.427
r_angle_other_deg0.841
r_chiral_restr0.082
r_bond_refined_d0.009
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2059
Nucleic Acid Atoms
Solvent Atoms432
Heterogen Atoms43

Software

Software
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
REFMACphasing