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Co-crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from Burkholderia pseudomallei with hydrolyzed CDP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3F0D pdb entry 3F0D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 289 34.4 mg/mL protein, Crystal ID 200564d9, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 1.98 37.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.078 α = 90 b = 66.457 β = 90 c = 131.465 γ = 90
Symmetry Space Group P 21 21 21
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 RIGAKU SATURN 944 2008-09-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54178
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 2.09 65.8 98.8 0.098 15.889 5.1 27899
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 2.09 2.18 98.4 0.549 2.5 4.3 2729
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 3F0D 2.09 50 27759 1406 98.35 0.2 0.197 0.1948 0.246 0.2404 RANDOM 31.043
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] 0.49 -0.01 -0.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.18 r_dihedral_angle_4_deg 13.916 r_dihedral_angle_3_deg 13.684 r_dihedral_angle_1_deg 4.962 r_scangle_it 1.811 r_scbond_it 1.097 r_angle_refined_deg 1.048 r_mcangle_it 0.847 r_mcbond_it 0.461 r_chiral_restr 0.068
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.18 r_dihedral_angle_4_deg 13.916 r_dihedral_angle_3_deg 13.684 r_dihedral_angle_1_deg 4.962 r_scangle_it 1.811 r_scbond_it 1.097 r_angle_refined_deg 1.048 r_mcangle_it 0.847 r_mcbond_it 0.461 r_chiral_restr 0.068 r_bond_refined_d 0.007 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3508 Nucleic Acid Atoms Solvent Atoms 203 Heterogen Atoms 31
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction