4Q06

Crystal structure of chimeric carbonic anhydrase IX 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
2.0338.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.015α = 90
b = 41.343β = 104.14
c = 72.194γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2013-05-21MSINGLE 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 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
11.14970.00691.40.06314.777799810.186
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)
11.151.21720.1890.18946.78923

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 3HLJ1.1540.747797877978791091.010.140.140.1370.168RANDOM17.922
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]
0.08-0.12-0.150.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.144
r_sphericity_free22.712
r_dihedral_angle_4_deg20.563
r_sphericity_bonded14.336
r_dihedral_angle_3_deg14.055
r_rigid_bond_restr8.976
r_dihedral_angle_1_deg7.018
r_angle_refined_deg2.448
r_chiral_restr0.168
r_bond_refined_d0.024
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.144
r_sphericity_free22.712
r_dihedral_angle_4_deg20.563
r_sphericity_bonded14.336
r_dihedral_angle_3_deg14.055
r_rigid_bond_restr8.976
r_dihedral_angle_1_deg7.018
r_angle_refined_deg2.448
r_chiral_restr0.168
r_bond_refined_d0.024
r_gen_planes_refined0.014
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2055
Nucleic Acid Atoms
Solvent Atoms292
Heterogen Atoms42

Software

Software
Software NamePurpose
REFMACrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction