9L2X | pdb_00009l2x

Zn-Carbonic Anhydrase II complexed with 3NPA under 15 atm CO2


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 9KIB 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.82931.3 M sodium citrate, 50 mM Tris-HCl
Crystal Properties
Matthews coefficientSolvent content
2.0740.48

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 41.971α = 90
b = 41.275β = 104.06
c = 72.041γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 9M2019-03-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPAL/PLS BEAMLINE 5C (4A)0.8856PAL/PLS5C (4A)

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
11.143095.10.0460.050.019141.66.883043
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)
11.141.1692.40.3050.3310.1250.9416.76.8

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-VALUE1.143078972402295.010.122060.120580.12090.152430.153RANDOM14.975
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]
0.48-0.28-0.09-0.22
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free59.292
r_dihedral_angle_2_deg33.573
r_dihedral_angle_4_deg21.398
r_sphericity_bonded17.52
r_dihedral_angle_3_deg12.264
r_long_range_B_refined8.53
r_long_range_B_other7.221
r_rigid_bond_restr7.166
r_dihedral_angle_1_deg7.1
r_scangle_other4.038
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free59.292
r_dihedral_angle_2_deg33.573
r_dihedral_angle_4_deg21.398
r_sphericity_bonded17.52
r_dihedral_angle_3_deg12.264
r_long_range_B_refined8.53
r_long_range_B_other7.221
r_rigid_bond_restr7.166
r_dihedral_angle_1_deg7.1
r_scangle_other4.038
r_scbond_it3.614
r_scbond_other3.613
r_mcangle_other3.247
r_mcangle_it3.218
r_angle_refined_deg2.738
r_mcbond_it2.56
r_mcbond_other2.535
r_angle_other_deg1.968
r_chiral_restr0.18
r_bond_refined_d0.032
r_gen_planes_other0.024
r_gen_planes_refined0.017
r_bond_other_d0.002
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 Atoms354
Heterogen Atoms7

Software

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