2C2N

Structure of human mitochondrial malonyltransferase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1MLAPDB ENTRY 1MLA

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.529332%PEG4000, 0.25M LI2SO4, 100MM TRIS-HCL, PH8.5, SITTING DROP, 293 K, pH 8.50
Crystal Properties
Matthews coefficientSolvent content
2.243.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.573α = 90
b = 84.828β = 93.43
c = 74.565γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMIRRORS2005-09-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SASLSX10SA

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
11.555299.40.0812.54940822
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)
11.551.6596.50.282.282.44

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 1MLA1.5574.3392079200599.50.1790.1780.218RANDOM13.62
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]
-0.06-1.66-0.650.51
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.231
r_dihedral_angle_4_deg13.901
r_dihedral_angle_3_deg13.791
r_dihedral_angle_1_deg5.177
r_scangle_it4.208
r_scbond_it2.734
r_angle_refined_deg1.652
r_mcangle_it1.591
r_mcbond_it1.084
r_nbtor_refined0.309
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.231
r_dihedral_angle_4_deg13.901
r_dihedral_angle_3_deg13.791
r_dihedral_angle_1_deg5.177
r_scangle_it4.208
r_scbond_it2.734
r_angle_refined_deg1.652
r_mcangle_it1.591
r_mcbond_it1.084
r_nbtor_refined0.309
r_symmetry_vdw_refined0.243
r_nbd_refined0.212
r_xyhbond_nbd_refined0.2
r_symmetry_hbond_refined0.149
r_chiral_restr0.11
r_bond_refined_d0.016
r_gen_planes_refined0.008
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4779
Nucleic Acid Atoms
Solvent Atoms575
Heterogen Atoms74

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing