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Crystal structure of EF-Pyl in complex with GMPPNP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.8 277 Na/Acetate, Na/Citrate, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.41 49.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.061 α = 90 b = 108.703 β = 90 c = 58.315 γ = 90
Symmetry Space Group P 21 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 2004-10-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 0.97943 Photon Factory BL-5A
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 1.7 50 99.9 44115 15.7
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 1.7 19.88 39680 4434 100 0.19328 0.18892 0.2333 0.2312 RANDOM 20.062
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] 0.05 -0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.986 r_dihedral_angle_4_deg 20.739 r_dihedral_angle_3_deg 14.237 r_dihedral_angle_1_deg 6.102 r_scangle_it 4.335 r_scbond_it 2.686 r_mcangle_it 1.607 r_angle_refined_deg 1.414 r_mcbond_it 1.046 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.986 r_dihedral_angle_4_deg 20.739 r_dihedral_angle_3_deg 14.237 r_dihedral_angle_1_deg 6.102 r_scangle_it 4.335 r_scbond_it 2.686 r_mcangle_it 1.607 r_angle_refined_deg 1.414 r_mcbond_it 1.046 r_nbtor_refined 0.303 r_symmetry_vdw_refined 0.217 r_nbd_refined 0.207 r_xyhbond_nbd_refined 0.177 r_symmetry_hbond_refined 0.175 r_chiral_restr 0.092 r_metal_ion_refined 0.071 r_bond_refined_d 0.012 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2765 Nucleic Acid Atoms Solvent Atoms 400 Heterogen Atoms 33
Software Software Software Name Purpose HKL-2000 data collection SOLVE phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling