5YUI

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 DROP2931.3M sodium citrate, 100mM TrisHCl pH 7.8
Crystal Properties
Matthews coefficientSolvent content
2.0941.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.281α = 90
b = 41.45β = 104.14
c = 72.105γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102008-12-21MSINGLE 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
11.250960.05630.46.769247
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)
11.21.2265.80.5961.93.3

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 REPLACEMENTTHROUGHOUT3D921.226.7269247368095.910.106140.104670.13395RANDOM13.961
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]
-0.01-0.010.02
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free54.482
r_dihedral_angle_2_deg32.515
r_dihedral_angle_4_deg24.637
r_sphericity_bonded12.011
r_dihedral_angle_3_deg11.181
r_dihedral_angle_1_deg6.8
r_long_range_B_refined6.097
r_rigid_bond_restr5.994
r_long_range_B_other4.348
r_scangle_other3.256
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free54.482
r_dihedral_angle_2_deg32.515
r_dihedral_angle_4_deg24.637
r_sphericity_bonded12.011
r_dihedral_angle_3_deg11.181
r_dihedral_angle_1_deg6.8
r_long_range_B_refined6.097
r_rigid_bond_restr5.994
r_long_range_B_other4.348
r_scangle_other3.256
r_scbond_it2.813
r_scbond_other2.813
r_mcangle_other2.001
r_mcangle_it1.988
r_angle_refined_deg1.982
r_mcbond_it1.529
r_mcbond_other1.506
r_angle_other_deg0.983
r_chiral_restr0.15
r_bond_refined_d0.022
r_gen_planes_refined0.012
r_bond_other_d0.002
r_gen_planes_other0.002
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 Atoms392
Heterogen Atoms13

Software

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