3E3F

H. influenzae beta-carbonic anhydrase, variant V47A with 100 mM bicarbonate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2A8DPDB ENTRY 2A8D

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52950.1 M HEPES, 0.7 M sodium potassium tartrate, 100 mM sodium bicarbonate, 12 mg/mL protein, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
3.160.29

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 83.897α = 90
b = 83.897β = 90
c = 184.867γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102007-04-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCHESS BEAMLINE F20.980CHESSF2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)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
12.376.47299.20.0660.06622.68.230001
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.32.4294.60.3670.3672.144077

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2A8D2.328.932992629926152399.130.1950.1950.1930.23RANDOM48.922
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]
0.590.59-1.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.785
r_dihedral_angle_4_deg20.729
r_dihedral_angle_3_deg18.639
r_dihedral_angle_1_deg6.839
r_scangle_it2.983
r_scbond_it2.192
r_angle_refined_deg1.566
r_mcangle_it1.363
r_mcbond_it1.132
r_angle_other_deg0.941
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.785
r_dihedral_angle_4_deg20.729
r_dihedral_angle_3_deg18.639
r_dihedral_angle_1_deg6.839
r_scangle_it2.983
r_scbond_it2.192
r_angle_refined_deg1.566
r_mcangle_it1.363
r_mcbond_it1.132
r_angle_other_deg0.941
r_symmetry_vdw_other0.293
r_nbd_refined0.23
r_symmetry_hbond_refined0.218
r_metal_ion_refined0.204
r_nbd_other0.198
r_xyhbond_nbd_refined0.19
r_mcbond_other0.184
r_nbtor_refined0.181
r_nbtor_other0.092
r_chiral_restr0.087
r_symmetry_vdw_refined0.081
r_xyhbond_nbd_other0.036
r_bond_refined_d0.017
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2894
Nucleic Acid Atoms
Solvent Atoms84
Heterogen Atoms22

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction