9GUM | pdb_00009gum

Human carbonic anhydrase II complexed with N-phenethyl-2-(1H-tetrazol-5-yl)acetamide


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP82961.5 M sodium citrate, 0.1 M Tris pH 8.0
Crystal Properties
Matthews coefficientSolvent content
2.1442.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.568α = 90
b = 41.876β = 104.732
c = 72.564γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2024-05-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONELETTRA BEAMLINE 11.2C1.00ELETTRA11.2C

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
11.741.292.70.1180.1380.9969.36.125464
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)
11.71.73780.8010.9510.6921.85.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)Mean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTNONE1.741.225364136392.350.1580.15330.16430.24770.243819.066
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]
1.851-0.395-0.823-0.721
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.686
r_dihedral_angle_4_deg22.492
r_dihedral_angle_3_deg15.396
r_dihedral_angle_1_deg7.597
r_rigid_bond_restr5.988
r_scangle_it5.192
r_scangle_other5.191
r_lrange_it5.165
r_lrange_other5.069
r_scbond_it4.251
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.686
r_dihedral_angle_4_deg22.492
r_dihedral_angle_3_deg15.396
r_dihedral_angle_1_deg7.597
r_rigid_bond_restr5.988
r_scangle_it5.192
r_scangle_other5.191
r_lrange_it5.165
r_lrange_other5.069
r_scbond_it4.251
r_scbond_other4.25
r_mcangle_it3.969
r_mcangle_other3.968
r_mcbond_it3.226
r_mcbond_other3.216
r_angle_refined_deg1.789
r_angle_other_deg1.358
r_nbd_refined0.218
r_symmetry_nbd_refined0.206
r_symmetry_nbd_other0.205
r_nbd_other0.197
r_nbtor_refined0.169
r_xyhbond_nbd_refined0.136
r_symmetry_xyhbond_nbd_refined0.135
r_metal_ion_refined0.093
r_chiral_restr0.088
r_symmetry_nbtor_other0.08
r_bond_refined_d0.013
r_gen_planes_refined0.01
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2051
Nucleic Acid Atoms
Solvent Atoms161
Heterogen Atoms22

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing