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Crystal structure of L. major mevalonate kinase in complex with R-mevalonate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Selenomethionine derivative of the L. major mevalonate kinase
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.2 291 1.2M sodium citrate, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.19 43.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.185 α = 90 b = 88.446 β = 103.51 c = 87.718 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 IMAGE PLATE RIGAKU RAXIS IV mirrors 2005-07-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU
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) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.7 39.253 95.6 0.07 0.07 9 4.1 39420 39420 1 1
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) Redundancy Number Unique Reflections (All) 2 2.11 89.4 0.297 0.297 2.5 3.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 Selenomethionine derivative of the L. major mevalonate kinase 2 36.49 39398 37398 1999 95.27 0.17905 0.1763 0.1791 0.23016 0.2313 RANDOM 22.353
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 35.927 r_dihedral_angle_4_deg 16.754 r_dihedral_angle_3_deg 13.412 r_dihedral_angle_1_deg 5.113 r_scangle_it 1.702 r_scbond_it 1.246 r_mcangle_it 0.991 r_angle_refined_deg 0.952 r_mcbond_it 0.644 r_nbtor_refined 0.293
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.927 r_dihedral_angle_4_deg 16.754 r_dihedral_angle_3_deg 13.412 r_dihedral_angle_1_deg 5.113 r_scangle_it 1.702 r_scbond_it 1.246 r_mcangle_it 0.991 r_angle_refined_deg 0.952 r_mcbond_it 0.644 r_nbtor_refined 0.293 r_nbd_refined 0.173 r_symmetry_vdw_refined 0.136 r_symmetry_hbond_refined 0.123 r_xyhbond_nbd_refined 0.107 r_chiral_restr 0.065 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5157 Nucleic Acid Atoms Solvent Atoms 695 Heterogen Atoms 10
Software Software Software Name Purpose SCALA data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction CCP4 data scaling