3KGQ

Carboxypeptidase A liganded to an organic small-molecule: conformational changes


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2CTBPDB ENTRY 2CTB

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP728920% PEG 3350, 0.2M NH4Cl, 0.02M Tris, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
1.9737.61

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 40.604α = 90
b = 57.006β = 102.04
c = 60.604γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR555 FLAT PANELMirrors2009-07-31MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X110.8150EMBL/DESY, HAMBURGX11

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
11.69820.67399.60.0780.07818.12.9295943325.4
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)
11.71.7999.80.280.2823.14288

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 2CTB1.720.24295942729689391.540.180.180.180.204RANDOM17.72
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]
0.030.22-0.210.27
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.565
r_dihedral_angle_4_deg15.692
r_dihedral_angle_3_deg11.408
r_dihedral_angle_1_deg5.33
r_scangle_it1.876
r_scbond_it1.147
r_angle_refined_deg1.042
r_mcangle_it0.795
r_mcbond_it0.423
r_chiral_restr0.074
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.565
r_dihedral_angle_4_deg15.692
r_dihedral_angle_3_deg11.408
r_dihedral_angle_1_deg5.33
r_scangle_it1.876
r_scbond_it1.147
r_angle_refined_deg1.042
r_mcangle_it0.795
r_mcbond_it0.423
r_chiral_restr0.074
r_bond_refined_d0.008
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2398
Nucleic Acid Atoms
Solvent Atoms214
Heterogen Atoms64

Software

Software
Software NamePurpose
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345dtbdata collection
AUTOMARdata reduction