3HUV

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, HANGING DROP7.529110% PEG8000, 0.02M tris, pH7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
1.9637.26

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.83α = 90
b = 56.98β = 100.25
c = 56.69γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2007-06-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X110.8148EMBL/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
11.955.81599.80.1640.1369.63.321281212632216.03
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)
1.921000.490.492.43.33091

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2CTB1.92122213122079745099.780.182650.181690.22703RANDOM18.045
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]
-0.34-2.16-1.160.73
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.137
r_dihedral_angle_3_deg14.77
r_dihedral_angle_4_deg11.75
r_dihedral_angle_1_deg5.521
r_scangle_it2.242
r_scbond_it1.424
r_angle_refined_deg1.182
r_mcangle_it0.931
r_mcbond_it0.514
r_chiral_restr0.078
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.137
r_dihedral_angle_3_deg14.77
r_dihedral_angle_4_deg11.75
r_dihedral_angle_1_deg5.521
r_scangle_it2.242
r_scbond_it1.424
r_angle_refined_deg1.182
r_mcangle_it0.931
r_mcbond_it0.514
r_chiral_restr0.078
r_bond_refined_d0.008
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2404
Nucleic Acid Atoms
Solvent Atoms222
Heterogen Atoms1

Software

Software
Software NamePurpose
MAR345dtbdata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling