4Q09

Crystal structure of chimeric carbonic anhydrase XII with inhibitor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3HLJPDB ENTRY 3HLJ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7291Crystallization buffer was 0.1M sodium BICINE, pH 9, 0.2 M ammonium sulfate and 2M sodium malonate pH 7 made from 1M sodium BICINE and 3.4M sodium malonate, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
1.9737.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 41.835α = 90
b = 41.011β = 103.56
c = 71.006γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2012-12-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)0.826606PETRA III, EMBL c/o DESYP13 (MX1)

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
11.269.0398.80.0420.04221.16.77241710.985
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)
11.21.2698.20.3460.3462.26.410431

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 DIFFRACTIONMRTHROUGHOUTPDB ENTRY 3HLJ1.269.037239972399724698.690.1430.1430.1390.178RANDOM17.485
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]
0.510.320.52-0.89
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.967
r_sphericity_free28.909
r_dihedral_angle_4_deg18.552
r_sphericity_bonded17.759
r_dihedral_angle_3_deg13.301
r_rigid_bond_restr7.641
r_dihedral_angle_1_deg7.204
r_angle_refined_deg2.333
r_chiral_restr0.16
r_bond_refined_d0.024
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.967
r_sphericity_free28.909
r_dihedral_angle_4_deg18.552
r_sphericity_bonded17.759
r_dihedral_angle_3_deg13.301
r_rigid_bond_restr7.641
r_dihedral_angle_1_deg7.204
r_angle_refined_deg2.333
r_chiral_restr0.16
r_bond_refined_d0.024
r_gen_planes_refined0.014
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2042
Nucleic Acid Atoms
Solvent Atoms252
Heterogen Atoms53

Software

Software
Software NamePurpose
REFMACrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
HKL-2000data collection
XDSdata reduction
MOLREPphasing