9L30 | pdb_00009l30

Zn-Carbonic Anhydrase II complexed with 3NPA at 140 K


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7Y2A 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.82931.3 M sodium citrate, 50 mM Tris-HCl
Crystal Properties
Matthews coefficientSolvent content
2.0640.33

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 41.911α = 90
b = 41.155β = 104.27
c = 72.232γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray140CCDRAYONIX MX225-HS2019-07-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPAL/PLS BEAMLINE 6D0.97934PAL/PLS6D

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
11.23099.50.0750.0880.0450.99215.73.674230
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)
11.21.2296.30.310.3780.2120.863.52.8

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-VALUE1.23070539367599.470.14650.144860.14540.179350.1807RANDOM14.592
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]
0.49-0.23-0.05-0.29
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free36.783
r_dihedral_angle_2_deg35.229
r_dihedral_angle_4_deg25.888
r_sphericity_bonded15.551
r_dihedral_angle_3_deg12.304
r_dihedral_angle_1_deg7.024
r_scangle_other5.744
r_long_range_B_refined5.682
r_long_range_B_other5.226
r_rigid_bond_restr5.163
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free36.783
r_dihedral_angle_2_deg35.229
r_dihedral_angle_4_deg25.888
r_sphericity_bonded15.551
r_dihedral_angle_3_deg12.304
r_dihedral_angle_1_deg7.024
r_scangle_other5.744
r_long_range_B_refined5.682
r_long_range_B_other5.226
r_rigid_bond_restr5.163
r_scbond_it4.922
r_scbond_other4.921
r_mcangle_other2.658
r_mcangle_it2.632
r_angle_refined_deg2.56
r_mcbond_it2.317
r_mcbond_other2.299
r_angle_other_deg1.228
r_chiral_restr0.177
r_bond_refined_d0.029
r_gen_planes_refined0.014
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 Atoms242
Heterogen Atoms14

Software

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