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Crystal structure of geranyltransferase from helicobacter pylori 26695
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 294 0.1M HEPES PH 7.5, 1500MM LITHIUM SULFATE, 10% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K
Crystal Properties Matthews coefficient Solvent content 2.9 57.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.04 α = 90 b = 123.844 β = 92.67 c = 111.617 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 93 CCD ADSC QUANTUM 315 MIRRORS 2010-01-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A NSLS X29A
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 2.299 40 99 0.1 6.5 3.7 71235 -5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.29 2.35 1.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 2.3 20 67956 2111 98.65 0.19714 0.1955 0.1955 0.25245 0.2485 RANDOM 59.727
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] -0.68 -2.5 -4.32 4.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.599 r_dihedral_angle_3_deg 18.99 r_dihedral_angle_4_deg 18.076 r_scangle_it 9.311 r_scbond_it 6.816 r_mcangle_it 5.689 r_dihedral_angle_1_deg 5.36 r_mcbond_it 3.975 r_angle_refined_deg 1.315 r_nbtor_refined 0.296
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.599 r_dihedral_angle_3_deg 18.99 r_dihedral_angle_4_deg 18.076 r_scangle_it 9.311 r_scbond_it 6.816 r_mcangle_it 5.689 r_dihedral_angle_1_deg 5.36 r_mcbond_it 3.975 r_angle_refined_deg 1.315 r_nbtor_refined 0.296 r_nbd_refined 0.16 r_symmetry_hbond_refined 0.16 r_xyhbond_nbd_refined 0.152 r_symmetry_vdw_refined 0.121 r_chiral_restr 0.095 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9185 Nucleic Acid Atoms Solvent Atoms 169 Heterogen Atoms 45
Software Software Software Name Purpose SHELX model building PHENIX model building RESOLVE model building REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling SHELX phasing PHENIX phasing RESOLVE phasing