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Ribosomal L30e of Thermococcus celer, P59A mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1H7M PDB ENTRY 1H7M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 10% PEG 6000 0.1M HEPES PH 7.0 20% PEG 400
Crystal Properties Matthews coefficient Solvent content 1.8 36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 23.194 α = 90 b = 53.802 β = 109.36 c = 34.174 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 100 IMAGE PLATE MARRESEARCH 2003-11-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.77 16.93 99.6 0.04 24.9 3.3 7622
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.77 1.86 98.6 0.08 11.7 3.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1H7M 1.77 32.27 7457 359 99.5 0.193 0.19 0.1977 0.248 0.249 RANDOM 12.18
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] -0.07 -0.3 -0.23 0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.841 r_dihedral_angle_3_deg 14.75 r_dihedral_angle_4_deg 11.313 r_dihedral_angle_1_deg 5.323 r_scangle_it 3.607 r_scbond_it 2.567 r_angle_refined_deg 1.467 r_mcangle_it 1.466 r_mcbond_it 1.324 r_angle_other_deg 0.809
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.841 r_dihedral_angle_3_deg 14.75 r_dihedral_angle_4_deg 11.313 r_dihedral_angle_1_deg 5.323 r_scangle_it 3.607 r_scbond_it 2.567 r_angle_refined_deg 1.467 r_mcangle_it 1.466 r_mcbond_it 1.324 r_angle_other_deg 0.809 r_nbd_refined 0.205 r_symmetry_vdw_other 0.201 r_xyhbond_nbd_refined 0.179 r_nbtor_refined 0.175 r_nbd_other 0.164 r_symmetry_hbond_refined 0.118 r_symmetry_vdw_refined 0.099 r_chiral_restr 0.091 r_nbtor_other 0.084 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 747 Nucleic Acid Atoms Solvent Atoms 87 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing