5YUK

CO2 release in human carbonic anhydrase II crystals: reveal histidine 64 and solvent dynamics


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3D92 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2931.3 M sodium citrate, 100 mM TrisHCl pH 7.8
Crystal Properties
Matthews coefficientSolvent content
2.0740.69

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.22α = 90
b = 41.244β = 104.19
c = 71.963γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102008-12-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCHESS BEAMLINE F20.9795CHESSF2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)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
11.45501000.07728.57.440706
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.451.481000.4383.97.3

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3D921.4524.5240706216199.850.09860.096540.13641RANDOM17.984
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
KeyRefinement Restraint Deviation
r_sphericity_free41.499
r_dihedral_angle_2_deg32.984
r_dihedral_angle_4_deg25.458
r_sphericity_bonded12.213
r_dihedral_angle_3_deg11.642
r_dihedral_angle_1_deg6.61
r_rigid_bond_restr5.372
r_long_range_B_refined5.346
r_long_range_B_other4.613
r_scangle_other4.007
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free41.499
r_dihedral_angle_2_deg32.984
r_dihedral_angle_4_deg25.458
r_sphericity_bonded12.213
r_dihedral_angle_3_deg11.642
r_dihedral_angle_1_deg6.61
r_rigid_bond_restr5.372
r_long_range_B_refined5.346
r_long_range_B_other4.613
r_scangle_other4.007
r_scbond_it3.739
r_scbond_other3.739
r_mcangle_other2.393
r_mcangle_it2.381
r_mcbond_it1.977
r_mcbond_other1.977
r_angle_refined_deg1.87
r_angle_other_deg0.95
r_chiral_restr0.141
r_bond_refined_d0.021
r_gen_planes_refined0.011
r_gen_planes_other0.003
r_bond_other_d0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2049
Nucleic Acid Atoms
Solvent Atoms271
Heterogen Atoms7

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing