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Crystal structure of Human mevalonate diphosphate decarboxylase
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 6.5 292 MES buffer, PEG5KMME, Ammonium Sulfate, NaCl, pH 6.5, VAPOR DIFFUSION, temperature 292K
Crystal Properties Matthews coefficient Solvent content 2.39 46.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.96 α = 90 b = 53.19 β = 107.25 c = 97.79 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 277 IMAGE PLATE RIGAKU RAXIS IV++ mirrors 2004-08-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.4 29.45 99 0.063 18.4 3.7 33621 2 44.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.4 2.44 97.9 0.474 2.9 3.7
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 PDB entry 1FI4 2.4 29.45 32586 3249 96.4 0.218 0.218 0.2143 0.274 0.2704 RANDOM 49.2
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] 1.64 3.42 4.65 -6.28
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.4 c_angle_deg 1.4 c_improper_angle_d 1.02 c_bond_d 0.007 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.4 c_angle_deg 1.4 c_improper_angle_d 1.02 c_bond_d 0.007 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot c_mcbond_it c_mcangle_it c_scbond_it c_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5674 Nucleic Acid Atoms Solvent Atoms 129 Heterogen Atoms 10
Software Software Software Name Purpose CNS refinement CrystalClear data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing