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Mevalonate diphosphate decarboxylase from Trypanosoma brucei
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FI4 PDB ENTRY 1FI4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 298 22% PEG 8000, 180mM ammonium sulfate, 100mM sodium cacodylate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.5 50
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.463 α = 90 b = 168.666 β = 118.78 c = 54.85 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 ADSC QUANTUM 4 mirrors 2004-04-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 0.939 ESRF ID14-4
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 1.8 42.18 99 0.106 0.106 4.3 6.1 74800 74805 2 2 24
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) 1.8 1.9 98 0.658 0.658 1.1 5.8 10804
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 (All) 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 PDB ENTRY 1FI4 1.8 42.18 74800 74800 3767 98.96 0.168 0.168 0.166 0.1758 0.208 0.2149 RANDOM 24.335
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] -0.81 -0.82 1.02 -1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.965 r_dihedral_angle_4_deg 18.041 r_dihedral_angle_3_deg 14.062 r_dihedral_angle_1_deg 6.161 r_scangle_it 3.897 r_scbond_it 2.776 r_mcangle_it 1.595 r_angle_refined_deg 1.558 r_mcbond_it 1.413 r_angle_other_deg 0.922
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.965 r_dihedral_angle_4_deg 18.041 r_dihedral_angle_3_deg 14.062 r_dihedral_angle_1_deg 6.161 r_scangle_it 3.897 r_scbond_it 2.776 r_mcangle_it 1.595 r_angle_refined_deg 1.558 r_mcbond_it 1.413 r_angle_other_deg 0.922 r_mcbond_other 0.263 r_symmetry_vdw_other 0.233 r_symmetry_vdw_refined 0.224 r_nbd_refined 0.213 r_symmetry_hbond_refined 0.21 r_nbd_other 0.198 r_nbtor_refined 0.181 r_xyhbond_nbd_refined 0.18 r_chiral_restr 0.095 r_nbtor_other 0.089 r_bond_refined_d 0.016 r_xyhbond_nbd_other 0.013 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5820 Nucleic Acid Atoms Solvent Atoms 712 Heterogen Atoms 30
Software Software Software Name Purpose SCALA data scaling AMoRE phasing DM phasing REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction