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Haloferax volcanii Malate Synthase Lead(II) complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3PUG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 magnesium chloride, glyoxylate, Tris, KCl, ammonium acetate, PEG 4500, glycerol, sodium acetate trihydrate
Crystal Properties Matthews coefficient Solvent content 3.37 63.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 155.353 α = 90 b = 155.353 β = 90 c = 139.412 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV Rigaku Varimax-HR 2009-03-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54
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 2.1 96.81 99.5 0.103 13.2 3.7 35791
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 2.1 2.18 100 0.374 3.6
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3PUG 2.1 96.81 35791 1880 99.22 0.18477 0.18308 0.1947 0.21668 0.2258 RANDOM 48.764
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.434 r_dihedral_angle_3_deg 16.214 r_dihedral_angle_4_deg 15.826 r_long_range_B_refined 9.256 r_long_range_B_other 9.229 r_scangle_other 7.332 r_dihedral_angle_1_deg 6.643 r_mcangle_it 5.38 r_mcangle_other 5.379 r_scbond_it 5.293
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.434 r_dihedral_angle_3_deg 16.214 r_dihedral_angle_4_deg 15.826 r_long_range_B_refined 9.256 r_long_range_B_other 9.229 r_scangle_other 7.332 r_dihedral_angle_1_deg 6.643 r_mcangle_it 5.38 r_mcangle_other 5.379 r_scbond_it 5.293 r_scbond_other 5.282 r_mcbond_it 4.304 r_mcbond_other 4.302 r_angle_refined_deg 1.916 r_angle_other_deg 0.944 r_chiral_restr 0.114 r_bond_refined_d 0.02 r_gen_planes_refined 0.011 r_gen_planes_other 0.002 r_bond_other_d 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2795 Nucleic Acid Atoms Solvent Atoms 254 Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling PHASER phasing PDB_EXTRACT data extraction HKL-2000 data reduction PHASER phasing