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Crystal structure of geranyltransferase from helicobacter pylori complexed with magnesium and isoprenyl diphosphate
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 0.1M HEPES PH 7.5, 2000MM AMMONIUM SULFATE, 10% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K
Crystal Properties Matthews coefficient Solvent content 4.7 73.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 191.87 α = 90 b = 191.87 β = 90 c = 127.053 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 93 CCD ADSC QUANTUM 315 MIRRORS 2010-07-15 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 2.3 40 100 0.11 8.3 7.6 105082 -5 57.956
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.35 100 0.6 6.8
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 2.4 40 89539 2772 99.7 0.2148 0.2139 0.2144 0.24293 0.2437 RANDOM 63.151
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] 0.36 0.36 -0.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39 r_dihedral_angle_3_deg 17.433 r_dihedral_angle_4_deg 12.083 r_scangle_it 9.486 r_scbond_it 6.351 r_dihedral_angle_1_deg 4.76 r_mcangle_it 4.47 r_mcbond_it 2.51 r_angle_refined_deg 1.133 r_chiral_restr 0.076
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39 r_dihedral_angle_3_deg 17.433 r_dihedral_angle_4_deg 12.083 r_scangle_it 9.486 r_scbond_it 6.351 r_dihedral_angle_1_deg 4.76 r_mcangle_it 4.47 r_mcbond_it 2.51 r_angle_refined_deg 1.133 r_chiral_restr 0.076 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined 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 9608 Nucleic Acid Atoms Solvent Atoms 224 Heterogen Atoms 152
Software Software Software Name Purpose SHELX model building RESOLVE model building REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling SHELX phasing RESOLVE phasing