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High resolution structure of Methanocaldococcus jannaschii L7AE
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RA4 PDB ENTRY 1RA4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 20% PEG 3350, 50mM HEPES, 10% isopropanol, 5% ethylene glycol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 2.14 42.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.665 α = 90 b = 48.869 β = 90 c = 51.914 γ = 90
Symmetry Space Group P 21 21 21
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 4 2003-07-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X26C 0.9000 NSLS X26C
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 1.44 27.58 100 0.079 31.5044 7.1 21176 19412 2 2 19.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.44 1.488 70.4 0.839 3.195 7 1249
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) Number Reflections (All) 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 PDB ENTRY 1RA4 1.45 27.63 2 2 22372 18451 962 95.64 0.184 0.13533 0.13225 0.19296 0.1977 RANDOM 14.082
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] -0.02 0.15 -0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.256 r_dihedral_angle_4_deg 34.465 r_sphericity_free 22.368 r_dihedral_angle_3_deg 19.046 r_scangle_it 11.591 r_scbond_it 8.974 r_dihedral_angle_1_deg 6.512 r_sphericity_bonded 6.009 r_angle_refined_deg 4.59 r_mcangle_it 4.586
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.256 r_dihedral_angle_4_deg 34.465 r_sphericity_free 22.368 r_dihedral_angle_3_deg 19.046 r_scangle_it 11.591 r_scbond_it 8.974 r_dihedral_angle_1_deg 6.512 r_sphericity_bonded 6.009 r_angle_refined_deg 4.59 r_mcangle_it 4.586 r_rigid_bond_restr 4.221 r_mcbond_it 4.185 r_angle_other_deg 2.24 r_mcbond_other 1.503 r_symmetry_hbond_refined 0.465 r_symmetry_vdw_refined 0.382 r_symmetry_vdw_other 0.368 r_nbd_refined 0.291 r_xyhbond_nbd_refined 0.285 r_chiral_restr 0.273 r_nbd_other 0.232 r_nbtor_other 0.124 r_bond_refined_d 0.063 r_gen_planes_refined 0.02 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 958 Nucleic Acid Atoms Solvent Atoms 173 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement MADNESS data reduction SCALEPACK data scaling EPMR phasing