2Y7F

Crystal structure of the 3-keto-5-aminohexanoate cleavage enzyme (Kce) from C. Cloacamonas acidaminovorans in complex with the substrate 3- keto-5-aminohexanoate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2Y7DPDB ENTRY 2Y7D

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18.530% PEG4000, 0.2 M MGCL2, 0.1 M TRIS-HCL PH 8.5
Crystal Properties
Matthews coefficientSolvent content
2.0239.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 98.5α = 90
b = 98.48β = 90
c = 103.18γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDADSC CCDKIRKPATRICK-BAEZ PAIR OF BI-MORPH MIRRORS2009-02-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSOLEIL BEAMLINE PROXIMA 1SOLEILPROXIMA 1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.7534.3999.60.0616.33.6101452319.93
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.751.8498.70.432.93.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 2Y7D1.7533.5101263506499.710.15090.14970.1736RANDOM20.95
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]
1.6107-2.97281.3621
RMS Deviations
KeyRefinement Restraint Deviation
t_omega_torsion4.08
t_other_torsion2.69
t_angle_deg0.99
t_bond_d0.01
t_dihedral_angle_d
t_incorr_chiral_ct
t_pseud_angle
t_trig_c_planes
t_gen_planes
t_it
RMS Deviations
KeyRefinement Restraint Deviation
t_omega_torsion4.08
t_other_torsion2.69
t_angle_deg0.99
t_bond_d0.01
t_dihedral_angle_d
t_incorr_chiral_ct
t_pseud_angle
t_trig_c_planes
t_gen_planes
t_it
t_nbd
t_improper_torsion
t_chiral_improper_torsion
t_sum_occupancies
t_utility_distance
t_utility_angle
t_utility_torsion
t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8505
Nucleic Acid Atoms
Solvent Atoms872
Heterogen Atoms45

Software

Software
Software NamePurpose
BUSTERrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing