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Crystal structure of DXR from Thermooga maritia, in complex with fosmidomycin and NADPH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 293 0.1M HEPES, 35% MPD, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.61 52.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.622 α = 90 b = 108.622 β = 90 c = 74.662 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 CCD ADSC QUANTUM 210 2008-04-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0000 Photon Factory AR-NW12A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 50 99.1 58727 58356
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 2.1 98.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) 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 2 40.72 58727 55490 2953 99.5 0.209 0.207 0.2066 0.24 0.2392 RANDOM 50.39
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] -0.1 -0.1 0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.332 r_dihedral_angle_4_deg 17.53 r_dihedral_angle_3_deg 16.931 r_dihedral_angle_1_deg 5.635 r_scangle_it 4.347 r_scbond_it 2.596 r_mcangle_it 1.714 r_angle_refined_deg 1.472 r_mcbond_it 1.06 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.332 r_dihedral_angle_4_deg 17.53 r_dihedral_angle_3_deg 16.931 r_dihedral_angle_1_deg 5.635 r_scangle_it 4.347 r_scbond_it 2.596 r_mcangle_it 1.714 r_angle_refined_deg 1.472 r_mcbond_it 1.06 r_nbtor_refined 0.309 r_xyhbond_nbd_refined 0.244 r_symmetry_vdw_refined 0.244 r_nbd_refined 0.215 r_symmetry_hbond_refined 0.143 r_chiral_restr 0.104 r_metal_ion_refined 0.088 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 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_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 5872 Nucleic Acid Atoms Solvent Atoms 113 Heterogen Atoms 135
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing