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Ligand-bound form of Arabidopsis medium/long-chain length prenyl pyrophosphate synthase (surface polar residue mutant)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3APZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6 295 18%(w/v) PEG3350, 0.17M Sodium thiocyanate, pH 6.0, vapor diffusion, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.47 50.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 115.961 α = 90 b = 115.961 β = 90 c = 385.874 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 CCD ADSC QUANTUM 315 2009-11-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1 Photon Factory BL-5A
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 2.65 30 98.8 0.048 28.3 3.7 83662 1 1 78.8
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 2.65 2.74 97.4 0.495 2.1 2.6 21336
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 3APZ 2.65 30 83456 4284 98.57 0.2247 0.222 0.2496 0.274 0.2851 RANDOM 77.543
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] -24.33 -24.33 48.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.942 r_dihedral_angle_3_deg 21.18 r_dihedral_angle_4_deg 19.769 r_dihedral_angle_1_deg 6.192 r_scangle_it 2.521 r_angle_refined_deg 1.472 r_scbond_it 1.442 r_mcangle_it 0.907 r_mcbond_it 0.459 r_chiral_restr 0.094
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.942 r_dihedral_angle_3_deg 21.18 r_dihedral_angle_4_deg 19.769 r_dihedral_angle_1_deg 6.192 r_scangle_it 2.521 r_angle_refined_deg 1.472 r_scbond_it 1.442 r_mcangle_it 0.907 r_mcbond_it 0.459 r_chiral_restr 0.094 r_bond_refined_d 0.011 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 19483 Nucleic Acid Atoms Solvent Atoms 695 Heterogen Atoms 248
Software Software Software Name Purpose PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection DENZO data reduction SCALEPACK data scaling HKL-2000 data scaling