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Structure of human mitochondrial malonyltransferase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MLA PDB ENTRY 1MLA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 32%PEG4000, 0.25M LI2SO4, 100MM TRIS-HCL, PH8.5, SITTING DROP, 293 K, pH 8.50
Crystal Properties Matthews coefficient Solvent content 2.2 43.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.573 α = 90 b = 84.828 β = 93.43 c = 74.565 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARRESEARCH MIRRORS 2005-09-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.55 52 99.4 0.08 12.5 4 94082 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.55 1.65 96.5 0.28 2.28 2.44
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1MLA 1.55 74.33 92079 2005 99.5 0.179 0.178 0.218 0.2822 RANDOM 13.62
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 -0.65 0.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.231 r_dihedral_angle_4_deg 13.901 r_dihedral_angle_3_deg 13.791 r_dihedral_angle_1_deg 5.177 r_scangle_it 4.208 r_scbond_it 2.734 r_angle_refined_deg 1.652 r_mcangle_it 1.591 r_mcbond_it 1.084 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.231 r_dihedral_angle_4_deg 13.901 r_dihedral_angle_3_deg 13.791 r_dihedral_angle_1_deg 5.177 r_scangle_it 4.208 r_scbond_it 2.734 r_angle_refined_deg 1.652 r_mcangle_it 1.591 r_mcbond_it 1.084 r_nbtor_refined 0.309 r_symmetry_vdw_refined 0.243 r_nbd_refined 0.212 r_xyhbond_nbd_refined 0.2 r_symmetry_hbond_refined 0.149 r_chiral_restr 0.11 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 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 Atoms Number Protein Atoms 4779 Nucleic Acid Atoms Solvent Atoms 575 Heterogen Atoms 74
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing