9F15 | pdb_00009f15

Carbonic anhydrase II variant with bound iron complex


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelAlphaFold 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.52930.2 M Na Acet, 0.1 M Na Cacod 6.5 pH, 30 %w/v PEG 8K
Crystal Properties
Matthews coefficientSolvent content
2.0640.38

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.344α = 90
b = 70.664β = 90
c = 146.349γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 XE 16M2023-12-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.9763DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim 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
11.9338.7593.410.160.1660.0450.99812.2913.117297
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.931.99985.811.3031.3580.3760.7112.0712.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE1.9338.751643985893.450.183540.180510.1830.241220.243RANDOM28.399
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]
0.04-0.01-0.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg14.326
r_dihedral_angle_2_deg11.37
r_dihedral_angle_1_deg7.435
r_long_range_B_other6.081
r_long_range_B_refined6.068
r_scangle_other4.993
r_scbond_it3.354
r_scbond_other3.344
r_mcangle_it3.341
r_mcangle_other3.339
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg14.326
r_dihedral_angle_2_deg11.37
r_dihedral_angle_1_deg7.435
r_long_range_B_other6.081
r_long_range_B_refined6.068
r_scangle_other4.993
r_scbond_it3.354
r_scbond_other3.344
r_mcangle_it3.341
r_mcangle_other3.339
r_mcbond_it2.499
r_mcbond_other2.492
r_angle_refined_deg1.81
r_angle_other_deg0.587
r_chiral_restr0.08
r_bond_refined_d0.009
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
r_dihedral_angle_4_deg
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2056
Nucleic Acid Atoms
Solvent Atoms104
Heterogen Atoms53

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing