9L31 | pdb_00009l31

Zn-Carbonic Anhydrase II complexed with 3NPA at 160 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
2.0740.44

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 41.948α = 90
b = 41.199β = 104.32
c = 72.246γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray160CCDRAYONIX 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
11.23099.60.0690.080.0410.99716.23.674716
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)
11.21.2297.30.3110.3770.2110.8623.62.8

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-VALUE1.23070925369099.60.145280.143640.1440.178050.1791RANDOM15.145
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]
0.46-0.230.03-0.33
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free47.95
r_dihedral_angle_2_deg35.21
r_dihedral_angle_4_deg24.741
r_sphericity_bonded15.491
r_dihedral_angle_3_deg12.223
r_dihedral_angle_1_deg7.038
r_scangle_other6.59
r_long_range_B_refined6.072
r_long_range_B_other5.664
r_scbond_it5.654
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free47.95
r_dihedral_angle_2_deg35.21
r_dihedral_angle_4_deg24.741
r_sphericity_bonded15.491
r_dihedral_angle_3_deg12.223
r_dihedral_angle_1_deg7.038
r_scangle_other6.59
r_long_range_B_refined6.072
r_long_range_B_other5.664
r_scbond_it5.654
r_scbond_other5.65
r_rigid_bond_restr5.343
r_mcangle_other2.804
r_mcangle_it2.794
r_angle_refined_deg2.606
r_mcbond_other2.477
r_mcbond_it2.474
r_angle_other_deg1.256
r_chiral_restr0.178
r_bond_refined_d0.03
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