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Crystal structure of Geranyltranstransferase (EC 2.5.1.10) (tm0161) from THERMOTOGA MARITIMA at 1.90 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RTR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION,SITTING DROP,NANODROP 10.5 277 0.2M NaCl, 20.0% PEG-8000, 0.1M CAPS pH 10.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.32 62.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 138.594 α = 90 b = 138.594 β = 90 c = 46.466 γ = 90
Symmetry Space Group P 43 21 2
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 2005-09-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.2 0.9801 ALS 8.2.2
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 1.9 29.62 100 0.062 0.062 7.4 6.9 36302
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 1.9 1.95 100 100 0.475 0.475 1.6 6
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 (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1rtr 1.9 29.62 36252 1807 99.92 0.17 0.17 0.169 0.203 0.2273 RANDOM 25.418
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] -0.77 -0.77 1.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.519 r_dihedral_angle_4_deg 17.102 r_dihedral_angle_3_deg 13.119 r_scangle_it 7.997 r_scbond_it 6.121 r_dihedral_angle_1_deg 4.471 r_mcangle_it 3.448 r_mcbond_it 2.517 r_angle_refined_deg 1.43 r_angle_other_deg 0.914
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.519 r_dihedral_angle_4_deg 17.102 r_dihedral_angle_3_deg 13.119 r_scangle_it 7.997 r_scbond_it 6.121 r_dihedral_angle_1_deg 4.471 r_mcangle_it 3.448 r_mcbond_it 2.517 r_angle_refined_deg 1.43 r_angle_other_deg 0.914 r_mcbond_other 0.591 r_symmetry_vdw_refined 0.421 r_symmetry_vdw_other 0.346 r_nbd_refined 0.258 r_xyhbond_nbd_refined 0.195 r_nbd_other 0.18 r_nbtor_refined 0.18 r_chiral_restr 0.094 r_symmetry_hbond_refined 0.094 r_nbtor_other 0.087 r_bond_refined_d 0.017 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2118 Nucleic Acid Atoms Solvent Atoms 171 Heterogen Atoms 53
Software Software Software Name Purpose REFMAC refinement SCALA data scaling PDB_EXTRACT data extraction MOSFLM data reduction CCP4 data scaling MOLREP phasing